infocus Magazine - Issue 76, December 2024

ISSUE 76 DECEMBER 2024

The 3D Pollen Library Collection at NIH3D: From Humble Beginnings to the Largest Open-Source Collection of Online 3D Pollen Models Worldwide Plumbing the depths: a close look at some microscopic sea-creatures A new web resource for diatom optical microscopy Creating an EM facility: A dual perspective

Plus...News, Calendar, Reviews, Reports 1

ISSUE 76 DECEMBER 2024

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contents features 4

The 3D Pollen Library Collection at NIH3D: From Humble Beginnings to the Largest Open-Source Collection of Online 3D Pollen Models Worldwide Anthony J. Hayes

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Plumbing the depths: a close look at some microscopic sea-creatures John Hutchison

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A new web resource for diatom optical microscopy Jonathan Crowther

82

Creating an EM facility: A dual perspective Erin Tranfield and Jon Moss

regulars 18 45 64 72 92 96

Calendar Journal of Microscopy New Member Welcome Office News Company News New Products

reports and other features 23

Microscopy: Advances, Innovation, Impact 2024 incorporating the RMS AGM and section AGMs 52 2024 Scientific Achievement Award-winners announced!

56 Latin America Bioimaging Meeting and LABIxSuperres 66 Spotlight on…Kim Findlay 78 RMS Technical Specialist Job Shadowing Program Report 88 High School student steals the show at M&M 2024 Poster session 90 ‘The Microscopists’ podcast tackles mental health in special episode 106 RMS Ambassador Rob Kesseler captures the wonder of seeds in his latest book

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MAGAZ I N E

infocus is the Magazine of the Royal Microscopical Society (RMS) – the only truly international microscopical society. The RMS is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy. infocus Magazine 37/38 St Clements Oxford, OX4 1AJ, UK Tel. +44 (0)1865 254760 Email: infocus@rms.org.uk Website: www.infocus.org.uk Scientific Editor Leandro Lemgruber, University of Glasgow, UK Editor Owen Morton Tel. + (0)1865 254763, Email: editor@infocus.org.uk Editorial Board Susan Cox, King’s College, London, UK Rebecca Higginson, Loughborough University, UK Myfanwy Adams, John Innes Centre, Norwich, UK Maadhav Kothari, Zeiss Microscopy, UK Hilary Sandig, Cancer Research, UK Trevor Almeida, University of Glasgow, UK Mark Rigby, Nikon UK Advertising Email: advertising@infocus.org.uk ISSN: 1750-4740 © 2024 Royal Microscopical Society infocus is published four times per year by the RMS. Designed and produced

by Creative Design. Reproduction in whole or in part without permission from the RMS is forbidden. Views expressed in the Magazine are those of the individual contributors and do not necessarily reflect those of the RMS.

RoyalMicroscopicalSociety @RoyalMicroSoc @RoyalMicroSoc

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ISSUE 76 DECEMBER 2024

FROM THE SCIENTIFIC EDITOR Dear Readers, It’s a well-worn cliché as the festive season hoves into view, but time certainly does seem to be flying!

Here we are already, with our fourth and final issue of infocus for 2024 – and (if we do say so ourselves) we have a bit of a ‘Christmas cracker’ for you to round off the year.

On a ‘unicellular’ theme, we have two excellent articles shining their respective lights on tiny organisms which have captured the imagination of generations of microscopists. RMS History Committee Chair John Hutchison takes us on a journey through time, charting the early fascination with foraminifera, and their diverse shell forms. Several beautiful examples are discussed – from the bottom of the deepest oceans to the abundant micro-fossils found in chalk and limestone.

Meanwhile Jonathan Crowther provides a fascinating overview of his recent project to create a web resource – or perhaps more accurately, an online museum - of eye-catching diatom images. Jonathan’s interest in diatom slides began as a means of testing the resolution of his microscope, but his fascination with “the little marvels” soon took on a life of its own.

Another colourful – and highly impressive – resource has been created by Tony Hayes and colleagues at Cardiff University’s Bioimaging Research Hub. At the time of writing, the 3D Pollen Library Collection contains more than 160 published 3D models of pollen grains and spores from 150+ species of plant! In this issue, Tony explains how the project came about and how it is helping drive research, teaching and science engagement.

Elsewhere, we hear dual perspectives from Jon Moss and Erin Tranfield on the trials and tribulations along the road to setting up an electron microscopy facility. We are also treated to some words of wisdom from former RMS Council Member Kim Findlay, as she looks ahead to her retirement in this issue’s ‘spotlight’ interview.

I hope you enjoy reading all our December content, and wish you a very happy Christmas and new year.

Slàinte!

Leandro Lemgruber

COVER IMAGE: Mercury Detection, by María Carbajo Sánchez, Universidad de Extremadura.

Shortlisted entry to the 2023 RMS Scientific Imaging Competition (Electron Microscopy, Physical Sciences category).The image corresponds to printed gold and carbon electrodes modified with gold nanoparticles, used for voltammetric mercury detection. Due to its toxicity, new electroanalytical methodologies are being investigated for the determination of mercury in different environmental matrices (rainwater, river water, wastewater, atmospheric dust and soils). Scanning Electron Microscope Quanta 3D FEG (FEI Company). Secondary electron imaging. 5000x magnification.

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ISSUE 76 DECEMBER 2024

The 3D Pollen Library Collection at NIH3D: From Humble Beginnings to the Largest Open-Source Collection of Online 3D Pollen Models Worldwide Anthony J. Hayes, Bioimaging Research Hub, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX.

Pollen Counts: A selection of 3D pollen models from the Bioimaging Hub’s NIH3D Pollen Library Collection curated by Dr Tony Hayes. The collection currently comprises 173 published, DOI-referenced surface-rendered 3D models of pollen grains and spores from 158 species of plant. All models are 3D printable and compatible with virtual reality and augmented reality immersive technologies. 1. meadow goat’s beard (Tragopogon pratensis); 2. cow parsley (Anthriscus sylvestris); 3. seaside arrowgrass (Triglochin maritima); 5. pumpkin (Cucurbita pepo); 6. heath milkwort (Polygala serpyllifolia); 7. common daisy (Bellis perennis); 8. common groundsel (Senecio vulgaris); 9. thyme-leaf sandwort (Arenaria serpyllifolia); 10. common dandelion (Taraxacum officinale); 11. green field speedwell (Veronica agrestis); 12. cuckoo flower (Cardamine pratensis); 13. bastard-toadlax (Thesium humifusum); 14. creeping bentgrass (Agrostis stolonifera).

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Keywords: pollen, palynology, 3D printing, virtual reality, augmented reality, pedagogy, science outreach.

Pollen Counts

using a compound light microscope is not a trivial

A fine dust to the naked eye, exquisite in

task. The shallow depth of field at high objective

microscopic form and fundamentally important to

magnifications means having to focus through the

life on earth. Pollen grains contain the male gametes

volume of multiple grains in differing orientations

(i.e., sperm cells) from a flower’s anther that are

to construct a mental picture of their overall 3D

essential for reproduction in seed-bearing plants

morphology. Conveying this information, particularly

thus are pivotal to the ecosystems and foods that

to a non-specialist, via a 2D photomicrograph or

we take for granted. As well as being critical to life,

schematic presents further challenges as the brain

pollen records the evolutionary course of plant

is more adept at directly processing 3D spatial

taxa in the geological strata, allowing scientists to

information than it is in having to extrapolate

understand and map environmental change; has

volume from flat 2D images.

relevance to forensic science, serving to establish links between objects, people and places; and represents a powerful allergen, causing hay fever in up to 30% of the world’s population. Without overstating the obvious, pollen counts.

Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) have emerged as powerful analytical tools in palynology as they allow an appraisal of 3D form at high resolution.

Whilst SEM provides excellent depth of focus

Pollen grains come in a staggering variety of

and extremely high (nanometre; nm) resolution

shapes and sizes. Their outer surface, or exine, is

of surface structure, CLSM has several practical

often highly ornamented with unique structural

advantages. First, CLSM is compatible with standard

features that allow palynologists – the scientists

palynological slide preparations and does not

who study pollen and spores - to accurately identify

require complicated preparatory procedures. As

the parent species.1 Pollen identification is a highly

a fluorescence-based imaging technique, CLSM

skilled process requiring years of training and

can exploit the intrinsic fluorescent properties

experience. Characterising and classifying pollen

(autofluorescence) of the pollen exine to image

Figure 1. The 3D Pollen Library collection at NIH3D. Screenshot of the web interface. NIH3D is the foremost open, community driven portal to download, share and create bioscientific and medical 3D models for 3D printing and interactive visualisation.

1 The interested reader is directed to ‘The Illustrated Pollen Terminology’ (Halbritter et al., 2018) for comprehensive descriptions of pollen grain types and morphologies.

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ISSUE 76 DECEMBER 2024

microstructure, thus readily facilitating taxonomic

licence, together with source CLSM data, supporting

discrimination in a non-disruptive manner (Castro

methodology and associated image art. Each entry

et al., 2010). Furthermore, many of the pollen

is linked to major palynological databases (PalDat,

stains routinely used in palynological research

Global Pollen Project and PollenWiki) as well as the

are also highly fluorescent (Atlagic et al., 2012),

Wikipedia website for general information about

therefore archival pollen samples from herbarium

individual plant species. The surface-rendered 3D

collections are also amenable to this technique.

digital meshes are readily scalable and can be used

Second, the optical sectioning capability of CLSM

in STEM activities including 3D printing and both

allows pollen grains to be sequentially sectioned

AR and VR, thus offering a multitude of sensory

through their volume at sub-micrometre (µm)

learning experiences within educational, research

intervals, or z-steps , yielding a dataset of image

and science outreach and engagement contexts.

slices, or ‘z-stack’, that permits visualisation of both

The 3D printed outputs are effective pedagogic

internal and external structure. Third, the volume

tools that facilitate haptic learning experiences with

information contained in the z-stack can be digitally

immediate relevance to blind or partially sighted

reconstructed in any given 3D orientation, thus

individuals.

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facilitating comprehensive appraisal of 3D form.

Four, when surface rendered as a 3D polygon mesh and provided the correct file format, CLSM data is compatible with 3D printing and immersive technologies such as virtual reality and augmented reality (VR and AR, respectively), thus offering the potential for powerful 3D learning experiences within research and educational contexts.

The 3D Pollen Library: a palynology resource not to be sneezed at We have developed and refined workflows as outlined above, to accurately 3D model pollen grains as well as other biological samples at various levels of scale. The resultant surface-rendered 3D pollen meshes have been curated into the largest publicly accessible collection for palynological research, educational purposes and scientific outreach worldwide. At the time of writing, the 3D Pollen Library Collection hosted via NIH3D contains 173 published, DOI-referenced 3D models of pollen grains and spores from 158 species of plant (Figure 1). All the 3D pollen models are free for download for non-commercial usage under a CC-BY-NC

This article reviews the development and progress of this 3D pollen resource and provides examples of how it has been used in a multitude of collaborative projects, for education, public engagement and also for societal enrichment purposes.

Big journeys begin with small z-steps Anyone who suffers from hay fever appreciates that pollen is literally everywhere. The sheer ubiquity of pollen, coupled with its striking diversity of form and prominent autofluorescence make it particularly attractive from a microscopical perspective. It was these properties that made pollen ideal for the methodology we were developing in 2015 aimed at creating tangible, physical 3D replica models of microscopic samples.

The experimental approach we adopted was reasonably straightforward. The autofluorescent profile/fluorescent staining characteristics of the pollen exine can easily be mapped using lambda (l; spectral) scanning (Donaldsen, 2020) thus CLSM acquisition parameters can readily be optimised for fluorescent signal collection. Z-stacks of optical sections are hence taken through grains at high

2 Z, refers to the focal axis of the microscope. The x-and y-axis represent the first two dimensions (width and height); the z-axis, the third dimension, denotes depth.

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Figure 2. Supersizing pollen: from microscopic grain to medieval mace ball. A. Pollen grain from sunflower (Helianthus annuus) is optically sectioned by confocal microscopy. B. Dataset is surface rendered as a 3D digital model; C. digital model is 3D printed (N.B., the crosshatch pattern is the internal scaffold, the outer struts are the external supports); D. the finished 3D print with external scaffold material removed.The choice of colour is entirely arbitrary.

resolution, observing Nyquist sampling criterion

print - a pollen grain from the common sunflower,

to capture accurate volumetric information for 3D

Helianthus annuus - emerged from its supporting

reconstruction. In our hands, a z-step of around

scaffold: a perfect doppelganger of a microscopic

0.3µm (i.e. 300nm) is typically employed using a x63

grain supersized from roughly 1/50th of a millimetre

Plan-Apochromat 63x/1.4 oil immersion objective

in diameter to the dimensions of a medieval mace

of a Zeiss LSM880 Airyscan confocal microscope,

ball! (Figure 2).

however this value can vary depending upon the grains occurring within a size range of 10-70µm in

Kinaesthetic learning: getting in touch with palynology

diameter. The resultant z-stack data is then surface

After demonstrating the initial proof of principle, I

rendered as a 3D digital polygon mesh, to reflect

wrote a short blog article on the Bioimaging Hub’s

the surface topography of the pollen grain, and the

news site to showcase the technique (Web link:

digital output converted into a format conducive

IN-FOCUS: Bigging It Up: 3D Printing to Change

to 3D printing and AR/VR visualisation (e.g., the

the Shape of Microscopy) where I mused that a

virtual reality modelling language world file format,

physical, tangible model would allow improved

wrl) using Bitplane’s Imaris image analysis software

3D

(Oxford Instruments). The surface rendered output

structures and would have considerable relevance

is further processed in MeshLab to reduce the size

in an educational environment, particularly for the

of the mesh and to remove visible scan lines via

partially sighted or blind, by permitting kinaesthetic

decimation and Laplacian smoothing, respectively,

(i.e., tactile) learning experiences. Serendipitously,

taking care to preserve topology. Digital meshes are

the article was read by a PhD student at the School

highly reproducible and scalable thus the models

of History, Archaeology and Religion at Cardiff

can be 3D printed to specification within the

University who then approached us for our help

hardware constraints of any 3D printer. We have

in generating 3D printed models of prehistoric

used affordable fused filament deposition (FFD)

pollen grains identified in soil strata sampled from

3D printing technology for our work; however, the

archaeological sites in south Wales3. The research

meshes can be fabricated into physical models using

was part of an ongoing public engagement project,

other additive manufacturing techniques (see Zhou

entitled ‘Footprints in Time‘ that addressed climate

et al., 2024). Despite the underlying simplicity of the

change patterns in local coastal environments.

technique, it was a huge thrill when our first 3D

This

size of the pollen grain being imaged, with most

conceptualisation

presented

an

of

these

exciting

microscopic

opportunity

to

3 the study of ancient pollen grains is referred to as paleopalynology; whilst palynostratigraphy deals with the description and interpretation of vegetational successions based on the identification of pollen in geological strata.

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ISSUE 76 DECEMBER 2024

further showcase the methodology and led to

sectioning microscopy (e.g., confocal, multiphoton

the establishment of a small 3D pollen reference

and lightsheet imaging modalities).The paper utilised

collection (Web link: IN-FOCUS: Development of a

a variety of samples, including pollen, and exploited

3D Printed Pollen Reference Collection) which was

both fluorescence and reflectance microscopy to

used for science outreach and public engagement

generate the 3D models. This helped to increase

activities both within and outside Cardiff University

the profile of our work and was followed by several

(Figure 3).

external collaborations with public organisations requiring 3D pollen models. These included the

More interest followed from Cardiff University’s School of Pharmacy with requests for 3D prints of pollen species identified in locally sourced honey as part of the Pharmabees nutraceutical research programme4. Buoyed by the interest and the growing potential for 3D printing, due to the increasing affordability and reliability of the technology, I published a short methodology paper in 2017 allowing researchers to create their own bespoke models of microscopic samples via optical

National Botanic Garden of Wales (Web link: IN FOCUS: Plastic Fantastic – Making Pollen for The National Botanic Garden of Wales), the UK Met Office (Web link: IN FOCUS: 3D Pollen Prints Not To Be Sniffed At - Printing Pollen for the Met Office), as well as the Smithsonian Institution’s National Museum of Natural History in the US (Figure 4).

In each instance, I created bespoke collections of 3D pollen prints based on the species and print specifications required.Typically, this meant sampling

Figure 3. Examples of some of the initial 3D pollen/spore reference collection created for the Footprints in Time project at Cardiff University.

A. black alder (Alnus glutinosa); B. silver birch (Betula pendula); C. white goosefoot (Chenopodium album); D. common hazel (Corylus avellana); E common ivy (Hedera helix), F. common oak (Quercus robur); G. Scots pine (Pinus sylvestris); H. European white water lily (Nymphaea alba); I. common daisy (Bellis perennis); J. common fern (Polypodium vulgare); K. common bulrush (Typha latifolia); L. peat moss (Sphagnum sp.)

4 melissopalynology is the field of palynology concerned with the study of pollen in honey to help identify the geographical location and genus of plants that honeybees have visited.

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Figure 4. The Bioimaging Hub’s 3D pollen models out in the wild. Examples of how the 3D pollen prints have been used for pedagogy and science outreach and engagement. A. 3D models of assorted honey pollen species created for the PharmaBees programme at Cardiff University.

B. 3D pollen model being used in a classroom environment (year 7) as part of the Pollen8 Cymru initiative. C-D. Pollen models created for the National Botanic Garden of Wales. C. Model of a dandelion (Taraxacum officinale) pollen grain being exhibited at the Royal Welsh Show. D. 3D pollen models used for public engagement at the Growing the Future Cymru Pollinator festival. E.The Met office explaining the link between pollen and hay fever at the Bluedot festival. F. Science Made Simple staff show off some of our 3D pollen models ahead of the Glastonbury festival. G. Heather Pardoe explains the importance of pollen at the After Dark science event at Amgueddfa Cymru (National Museum of Wales).

Photographs courtesy of Mike Pascoe (B), Faye Watson (C, D), Felicity Liggins (E), Jack Laird (F) and Heather Pardoe (G).

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pollen in the field, performing the imaging and 3D

and education programmes and exhibited at various

modelling and then generating the finished 3D

culturally significant national and international

printed output on the facility’s UltiMaker FFD 3D

events such as the National Eisteddfod of Wales,

printer.The collections produced were used by each

The Royal Welsh Festival, Glastonbury, as well as

of the above organisations in their public outreach

smaller, local festivals, events and initiatives (e.g.,

ISSUE 76 DECEMBER 2024

Figure 5. Virtual reality (VR) pollen resource developed by the Bioimaging Research Hub.The VR resource allows users to interact with pollen grains and other 3D objects in different virtual learning environments. A-C. Interactive 3D pollen exhibit. A.Working prototype using the firstgeneration Oculus Go headset (2019) – one hand and three degrees of freedom movement (pitch, yaw and roll). B-F. updated and improved version using the second-generation Oculus Quest headset (2020) – two handed and six degrees of movement (also includes surge, heave, sway). D, E. Fun VR learning environments designed for children: 3D pollen pit, F. 3D pollen cannon. Unreal engine coding by Marc Isaacs and Angelina Murphy. G. An undergraduate student gets to grips with the VR controls during filming of a promotional video for Cardiff University at the Bioimaging Hub. H.Testing the VR at a research day at City Hall, Cardiff. Figure 4G courtesy of Rhys Jones, Cardiff University.

Between the Trees, Pollen8 Cymru, etc) generating significant interest from the public. Feedback from these was shared on the Bioimaging Hub’s X (formerly twitter) feed @cubioimaginghub.

Immersive learning: probing the reality of nature In 2019, the Bioimaging Research Hub began developing workflows that would allow virtual reality (VR) interaction with our surface rendered

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Figure. 6. Screenshot from the 3D Pollen Library collection showing a small selection of thumbnails of 3D pollen models available for download.

The collection currently holds 173 published, DOI-referenced models of pollen grains and spores from 158 species of plant, together with source data (confocal z-stacks), published supporting methodology, and links to major palynological databases for cross-referencing.The models and supporting data are free to download and to use for non-commercial purposes under a CC-BY-NC copyright licence.

3D digital models (Figure 5). This coincided with the release of the Oculus Go VR headset, which was the first affordable untethered headset to take VR mainstream. We used this device, and

The consequence of covid: the 3D pollen library collection and augmented reality The covid pandemic had enormous societal impact

the later Oculus Quest headset, in conjunction

worldwide, profoundly affecting human interaction

with the Unreal Engine to create and populate

and resulting in a huge shift to the digital realm.

VR environments with our entire range of 3D

The lockdowns and subsequent social distancing

digital models (Web link: IN FOCUS: Immersive

measures introduced by the Welsh Government

microscopy – 3D Visualisation and Manipulation

over this period effectively prevented us from

of Microscopic Samples Through Virtual Reality).

utilising the 3D printed pollen models or the VR

In addition to the 3D pollen models, we were

headset for public engagement or pedagogy in

also experimenting with 3D photogrammetry

group-based learning environments due to the

techniques in collaboration with the Wales Centre

infection risks posed. A different approach was

for Anatomical Education to create highly realistic

therefore necessary. Up until this point, all our 3D

3D models of anatomical samples for use in

digital pollen models were held on the Bioimaging

anatomy teaching (example here).

Hub’s internal server, thus it made sense to now make them freely available for non-commercial

The VR pollen resource, along with the 3D prints,

usage, under a Creative Commons CC-NY-NC

were employed for public engagement activities

licence, via the recently redeveloped NIH3D

within the School of Biosciences during Cardiff

website (formerly the NIH3D print exchange). The

University open days, UCAS visits etc until March

NIH3D website is the foremost open, community

2020. And then covid happened.

driven portal to download, share and create bioscientific and medical 3D models for 3D printing

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ISSUE 76 DECEMBER 2024

and interactive and immersive visualisation. This

A second consequence of covid was that it pushed

decision made the collection truly international in

us into developing new workflows to allow AR

its scope. Interested parties could download the

visualisation of our 3D pollen models (Figure

models, together with supporting metadata, directly

8). Critically, unlike VR, this technology does not

to their computers or personal devices for 3D

require a head set and hand controller(s), only a

visualisation, 3D printing or immersive experiences

personal smartphone or tablet, thus overcoming the

from anywhere in the world without the infection

potential risks associated with equipment sharing.

risk associated with a shared physical resource. We

AR also allows users to experience a photorealistic

were also able to work collaboratively with the

environment via the smart device’s camera output,

NIH3D development team and contribute to the

with generated perceptual information overlaid

look and feel of the new site.This partnership led to

upon it, thus providing a more natural immersive

the curation of our datasets into a special 3D Pollen

experience than the artificial environments of VR.

Library collection (Figures 6 and 7).

Furthermore, freed from the physical encumbrance of a VR headset, the user has a greater awareness of

Figure 7. The 3D engine for model visualisation on the NIH3D website. This example shows a pollen grain from thyme-leaf sandwort (Arenaria serpyllifolia).The display can be toggled between 2D and 3D modes.The 3D display presents the option of viewing the pollen grain as a surface rendered model (green) or wireframe (polygon mesh). Both views are shown here.The 3D model can be manipulated on screen into any desired orientation via rotate, drag, and zoom controls allowing visualisation of both external and internal structure (internal detail shown in lower figures). Description and links shown top right; download options, bottom right.

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Figure 8. Augmented reality (AR) visualisation of pollen grains. A-C. Snapshots taken from an android smartphone running a free AR app.

Ambient lighting and shadow effects make for a highly realistic immersive experience.The 3D pollen models can be freely moved, rotated and zoomed via the smartphone’s touchscreen interface and also circumnavigated and explored - both externally and internally - via directional information from the device’s sensors (i.e., accelerometer, gyroscope and compass). A. a pollen grain from ox-eye daisy (Leucanthemum vulgare) skews the proportions – whilst protecting the modesty - of Leonardo’s Vitruvian man. B. a dandelion (Taraxacum officinale) pollen grain, supersized as a gilded colossus. C. a pollen grain from common daisy (Bellis perennis) skinned in metallic silver.

Figure 9. A, B. Exhibit showing wheat pollen plush for visually impaired and blind.The exhibit, created by Alona Nesterenko, was part of the Ukrainian refugee art exhibition at the These3Streams Art festival at Llantwit Major. C. Surface rendered digital model of pollen grain from wheat (Triticum aestivan) which the plush was based upon.The pollen plush is approximately 20cm in diameter, whilst the pollen grain is approximately 50µm in diameter. Photographs A & B courtesy of Alona Nesterenko.

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Figure 10. Breaking the mould: supersizing pollen grains into gigantic public art sculptures. A. Concept art for the 3D pollen sculptures, copyright Saara Ekström. B-D. 3D pollen models from the NIH3D pollen collection to be made into concrete sculptures: B. blue passionflower (Passiflora caerulea), C. thyme (Thymus vulgaris), D. black elderberry (Sambucus nigra), E. ragweed (Ambrosia sp.). F, G. Examples of the casting moulds for the ragweed pollen sculpture. CAD (computer Aided Design) software is used to program a sculpting tool that mechanically carves a negative form of the pollen grain out of high density styrofoam blocks to create the moulds. A flat base, visible in F, is introduced into the mould to ensure that the sculpture remains stable. Eco-friendly natural concrete is poured into the moulds for each of the pollen species. When cured, the moulds are removed from the concrete sculptures. H-K concrete sculptures of ragweed (H, I) and thyme (J, K) pollen.The ragweed pollen sculpture (H-K) is one metre in diameter weighing approximately one and a quarter tonne.The individual shown in I demonstrates the enormous scale of the sculpture (approximately 500,000x larger than the source grain). Steel reinforcing rebar is visible in K. After the sculptures are freed from their moulds, they are hand finished and a coloured protective coating is added. L-N.The sculptures are then transported to the exhibition site and carefully lowered into place under ambient lighting, as demonstrated in concept art. Photographs A, F-N courtesy of Saara Ekström.

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their surroundings and is less likely to experience

3D pollen models to create sensory plush models

motion/simulation sickness (Web link: IN FOCUS:

for the visually impaired and blind. One of these,

AR Palynology: Probing the Reality of Nature/

a wheat pollen plush, dedicated to Ukraine, was

Nature of Reality).

recently exhibited at a local arts festival (Figure 9).

Amgueddfa Cymru: digitising the National Museum’s palynology collection.

Currently, we are collaborating with Finnish visual artist and film maker, Saara Ekström, who is supersizing four of our 3D pollen models into

Over the last year, the Bioimaging Hub has collaborated with Heather Pardoe, the principal botany

curator

and

senior

palynologist

at

Amgueddfa Cymru (the National Museum of Wales), to digitise their archival pollen collection.

This successful collaboration has significantly increased the number of pollen models that are now available through the 3D pollen library collection, almost doubling our content, and these

elementary school in Helsinki (Figure 10) – a brilliant way to enrich communal spaces, stimulate young (and old) minds and to increase awareness of the unseen natural world. This work was commissioned by the City of Helsinki and will be administered by the Helsinki Art Museum who are responsible for the city’s public art collection (Web link: IN FOCUS: Breaking the mould: Supersizing Pollen Grains as

have been incorporated into a subcollection of the

Gigantic Concrete Public Art Sculptures).

library, Amgueddfa Cymru, National Museum of

Current and future directions

Wales, palynology collection. I have also curated a small selection of models to highlight the range of interesting pollen morphologies present within the broader collection, 3D Pollen Library highlights.

Usage of the NIH3D Pollen Library

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gigantic concrete public art sculptures for an

The 3D pollen library collection at NIH3D has been an effective mechanism for dispersal of our 3D pollen models at an international level and we hope to improve and develop the site going forward.

We are continuing with our ongoing collaboration with Amgueddfa Cymru and are open to new

Following the establishment of the 3D Pollen library

partnerships to exploit and expand the 3D pollen

collection at NIH3D, the supported models and

resource for novel applications, activities and events

their supplementary metadata (confocal z-stacks

in research, teaching and science engagement, as

etc) have been viewed and downloaded many

well as for societal enrichment purposes (e.g., public

hundreds of times. Other than the number of views

art, exhibitions etc). As a microscopist, unveiling

and downloads per 3D mesh, we rely on direct

the unseen beauty of the microscopic world and

feedback from the user community to inform where

stimulating and promoting scientific enquiry remains

and how our models are being used. Feedback

a passion. There are now many publicly accessible

from users indicate that the resource is being used

science discovery centres in the UK dedicated

worldwide for a variety of purposes. Two recent

to STEM learning, with the longest established

usage examples include the University of Medellin,

centre, Techniquest, being based at Cardiff Bay.

Columbia who have utilised some of our 3D pollen

These discovery centres are united by a national

models for their palaeoecology classes, and the

charity, the Association for Science and Discovery

Beringia Interpretive Centre, Yukon, Canada, who

Centres (ASDC), which plays an important strategic

have exhibited our models as part of an interactive

role in the nation’s engagement with science. I am

display featuring pollen from pre- and post-glacial

currently looking into collaborative opportunities

periods. Recently we have supported local artist,

and partnerships that would allow the 3D pollen

Alona Nesterenko, in her studies at Cardiff College

models to be utilised in novel STEM activities in

Art Academy, who has drawn inspiration from our

these public learning environments. One exciting

ISSUE 76 DECEMBER 2024

area might be the development of new workflows

(Amgueddfa Cymru), Rhys Jones (School of

to facilitate mixed reality immersive imaging of

Biosciences, Cardiff University) and artists Saara

pollen grains. For example, the new Meta Quest 3

Ekström and Alona Nesterenko. Last, but certainly

mixed reality VR headset has opened the potential

not least, I would like to thank Kristen Brown at

for next level immersive experiences. The headset

NIH3D for her help and ongoing support in the

combines the advantages of VR and AR, with full

development of the 3D Pollen Library resource.

colour, high-resolution ‘passthrough’ technology which enables mixed reality (i.e., the blending of the real and computer-generated worlds) with enhanced hand tracking features, thus reducing the need for a hand controller and allowing a more natural immersive experience. New additive manufacturing techniques also offer the potential to 3D print at large scale at much higher print resolutions, and advances in computer aided design (CAD) open up new possibilities in the analysis, modification and optimisation of 3D design for STEM in the development of scientific learning resources, and also for public engagement and societal enrichment through ‘Sci-Art’. Lastly, new 3D imaging modalities providing faster speeds, higher throughput and greater resolution, coupled with AI deep learning will provide a step change in palynology research, allowing high throughput screening and rapid phenotyping of pollen samples across multiple scientific disciplines. It’s fair to say that the pollen forecast is looking good!

Acknowledgements Thanks to Bioimaging Research Hub staff, Marc Isaacs, and Claire Gealy, for contributions to the development of the 3D pollen resource and proofreading of this manuscript. Thanks also to Iain Perry, Jenn-Yeu Szeto and Peter Watson for assistance with the 3D printing. The Unreal Engine coding for the VR pollen resource was by Marc Isaacs and Angelina Murphy. A big thank you to Heather Pardoe for making the Amgueddfa Cymru archival pollen slide collection available to this project. I am also grateful to the following people for providing the feedback and usage examples highlighted in this manuscript: Faye Watson (National Botanic Garden

References

1. Halbritter, H., Ulrich, S., Grimsson, F., Weber, M., Zetter, R., Hesse, M., Buchner, R., Svojtka, M., Frosch-Radivo, A. (2018) Illustrated Pollen Terminology. Second edition. Springer ISBN: 9783-319-71364-9 (e-book); doi: 10.1007/978-3-31971365-6.

2. Donaldson, L. (2020) Autofluorescence in plants. Molecules. 25(10): 2393. DOI: 10.3390/ molecules25102393 3. Castro, A.J., Rejón, J.D., Fendri, M., JiménezQuesada, M.J., Zafra, A., Jiménez-López, J.C., Rodríguez-García, M.I., Alché, J.D. (2010) Taxonomical discrimination of pollen grains by using confocal laser scanning microscopy (CLSM) imaging of autofluorescence. In: Microscopy: Science, Technology, Applications and Education (pp.607-613), Edition: 2010. Chapter: 13.

Publisher: Formatex. Eds: Méndez-Vilas A., Díaz, J. 4. Atlagić, J., Terzić, S., Ana Marjanović-Jeromela, A. (2012) Staining and fluorescent microscopy methods for pollen viability determination in sunflower and other plant species. Industrial Crops and Products. 35 (1): 88-91. DOI: 10.1016/j. indcrop.2011.06.012.

5. Zhou, L., Miller, J., Vezza, J., Mayster, M., Raffay, M., Justice, Q., Tamimi, A.A., Hansotte, G., Sunkara, L.D., Bernat, J. (2024) Additive Manufacturing: A Comprehensive Review. Sensors 2024, 24: 2668.

DOI: 10.3390/s24092668.

6. Perry, I., Szeto, J-Y. A., Isaacs, M.D., Gealy, E.C., Rose, R., Scofield, S., Watson, P.D., Hayes, A.J. (2017) Production of 3D printed scale models from microscope volume datasets for use in STEM education. EMS Eng Sci, 2017, 1(1):002.

of Wales), Mike Pascoe (School of Pharmacy, Cardiff University), Felicity Liggins (UK Met Office), Jack Laird (Science Made Simple), Heather Pardoe

17

Calendar We are very pleased to continue offering a range of ‘in-person’ and virtual events this year, in order to maximise accessibility and provide opportunities to those who might not otherwise be able to attend.

The following information was correct at the time infocus went to print but could potentially be subject to change in the coming weeks. Please visit our event calendar at www.rms.org.uk for the latest updates.

If you have any questions about a booking you have already made for an event, or need any help or advice, please contact us at info@rms.org.uk

2024 December 5–6

Virtual European Flow Core Meeting 2024, (Online)

6

Super-resolution in the North 2024, Leeds, UK (RMS-hosted event)

11 Probing Magnetic Topologies with Corrected Lorentz STEM, London, UK

2025 January 6–7

UK Light Microscopy Facility Meeting 2025, Bristol, UK

8 – 9 Flow Cytometry Facilities Meeting 2025,

Edinburgh, UK

February

6 – 7 EM-UKI 2025, Liverpool, UK

March 3–6

Virtual Flow Cytometry Data Analysis Course Spring 2025, (Online)

10

Virtual Flow Cytometry Data Analysis Course Spring 2025 - Clinical Module, (Online)

24 – 27 Physics of Life, Harrogate, UK (RMS Exhibiting at event) 26 – 28 flowcytometryUK 2025, Newcastle, UK 31 March – 4 April

Electron Microscopy Spring School 2025,

Leeds, UK

April 1–2

EBSD 2025, Glasgow, UK

8 – 9 Introduction to Image Analysis 2025, Galway, Ireland (RMS-hosted event)

May

14 – 16 Advanced imaging techniques in biomineralisation research Faraday Discussion, Edinburgh, UK (RMS sponsored event)

June / July 9 – 10

Light Microscopy Summer School 2025, York, UK

11 – 12 Getting the most from your Confocal Course 2025,York, UK 30 June – 3 July mmc2025: Microscience Microscopy Congress 2025, Manchester, UK

For further information on all these events, please visit our Event Calendar at www.rms.org.uk

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Featured RMS events EM-UKI 2025 6 – 7 February, Liverpool, UK Committee Chair and 2025 Hosts: Heath Bagshaw and Alison Beckett, University of Liverpool The EM-UKI community meetings are an open forum for discussion of the latest developments and challenges in the field, suitable for both academic and commercial microscopists. The

Virtual Flow Cytometry Data Analysis Course Spring 2025 3 – 6 March (Online) Scientific organisers: Dan Payne, James Cook University Hospital; Derek Davies, Derek Davies Cytometry; Karen Hogg, Peter O’Toole and Sukhveer Kaur Mann, University of York This course will run over four half-days from Monday 3 March to Thursday 6 March 2025, plus one optional additional Clinical Module on Monday 10 March 2025. The course will cover the basics of analysis for a number of different applications including antibody phenotyping, DNA and cell cycle kinetics, cell proliferation and death, and functional studies. There will also be the opportunity to explore high-dimensional analysis using dimensionality reduction and clustering techniques.

meeting will include Techno Bites, talks, and discussions, and also hosts the RMS annual EM lecture.

This year’s programme will include the following sessions: • • • • •

RMS EM Lecture Updates from the EM Community Funding Careers & Outreach Interactive Methodology

Pre-recorded lectures will be provided in advance of the course with live small group practical sessions in the afternoons. It will run in the afternoon UK time to make it more accessible to those in other time zones (14:00 GMT/15:00 CET/09:00 EST). The Clinical Module on Monday 4 March 2024 will be a full day UK time (09:00 GMT/10:00 CET/04:00 EST).

Delegates will be able to use data files (which will be provided) and follow along with directed analysis by the course demonstrators. Analysis will be performed in either FlowJo or FCS Express and applications specialists will also form part of the demonstrator team.

This course is open to all and is suitable for those who are relatively new to flow cytometry and those who wish to expand their experience with applications and specific analysis.

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flowcytometryUK 2025 26 – 28 March, Newcastle, UK Scientific organisers: Derek Davies, Derek Davies Cytometry; Rachael Walker, Babraham Institute This meeting will consist of themed plenary sessions with talks from invited speakers.

There will also be parallel scientific workshops organised by members of the cytometry Electron Microscopy Spring School 2025 31 March – 4 April, Leeds, UK Scientific organisers: Louie Aspinall, Nicole Hondow, Rik Brydson, University of Leeds

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community and parallel commercial workshops.

There will be a large exhibition and the opportunity to network with flow and image cytometrists from all over Europe and beyond.

The meeting will highlight advances in flow and image instrumentation, high content screening, cancer and stem cell biology, applications of clinical cytometry and the development of novel probes and approaches in many areas of biomedical research.

The Electron Microscopy Spring School aims to provide a basic training in both the theory and practice of scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The course covers imaging, diffraction and chemical microanalysis as well as the highly important area of sample preparation.

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R E P O RT

Microscopy: Advances, Innovation, Impact 2024 - incorporating the RMS AGM & Section AGMs 2 October, Royal Society of Chemistry, Burlington House, London

T

he RMS would like to thank everyone who attended Microscopy: Advances, Innovation, Impact 2024 - incorporating the RMS AGM & Section AGMs. The free event, held in the heart of London at the Royal Society of Chemistry on 2 October, featured AGMs for each of the Society’s Science

sections, fascinating talks from leading researchers, and a number of award presentations.

It also included a series of quick-fire talks from the shortlisted candidates for the RMS Early Career Award – with the winner announced at the close of the meeting (see below).

possible to both RMS members and non-members.

Invited speakers included Dr Rob Harniman of the University of Bristol, who received the RMS Vice President’s Award for his work leading the

More than 70 people attended in person with a

Atomic Force Microscopy (AFM) facility at Bristol

further 50 logging on to follow proceedings online,

University’s School of Chemistry.

as part of efforts to make the event as accessible as

We also heard fascinating scientific talks from

The courtyard area outside the Royal Society of Chemistry, within Burlington House.

23

RMS President Peter O’Toole welcomes attendees.

Rob Harniman receives the RMS Vice President’s Award from former Vice President Susan Anderson.

24

Giulia Zanetti of Birkbeck College, Adriana Flores-

Heath (University of Leeds). Elsewhere, an equity,

Langarica (University of Birmingham) and George

diversity and inclusion-themed talk was delivered by

ISSUE 76 DECEMBER 2024

The courtyard area outside the Royal Society of Chemistry, within Burlington House.

Susan Anderson (left) receiving a gift from RMS Executive Honorary Secretary Michelle Peckham (centre) and Chief Executive Sali Davis, after stepping down from the RMS Executive Committee.

25

Mark Pickering (left) receiving the 2024 RMS Chris Hawes Award for Outreach and Education from RMS Hon Sec for Education Kerry Thompson.

Susan Cox receiving the RMS Scientific Achievement Award from Peter O'Toole.

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Roland Kroger receiving the RMS Scienetific Achievement Award.

Bernd Gotsmann was also among the RMS Scientific Achievement Award-winners to receive their award in person.

27

Akaash Kumar receives the 2024 RMS Early Career Award from Susan Anderson.

Dr Georgina Fletcher of BioimagingUK, examining

after 15 years’ service; and RMS Events Director

gender, class and other biases within the scientific

Tor Masters, who recently marked her 20th

community.

anniversary at the Society. The event concluded

We were delighted to welcome three of our 2024 Scientific Achievement Award-winners – Dr Susan Cox (King’s College London), Professor Roland Kröger (University of York) and Dr Bernd Gotsmann (IBM Research GmbH) to receive their awards. Meanwhile, Dr Mark Pickering (University College Dublin), received the 2024 Chris Hawes Award for Outreach and Education.

In addition, special presentations were made for Professor Susan Anderson, who has stepped down from the RMS Council and Executive Committee

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with the climax of the 2024 RMS Early Career Award Competition, in which three shortlisted candidates – Dr Akaash Kumar (MRC Laboratory of Molecular Biology & University of Cambridge), Dr Liam Rooney (University of Strathclyde) and Harshith Bachimanchi (University of Gothenburg), gave talks about their research. After some tricky deliberations by the judges, Akaash emerged as the winner for his presentation about his PhD work on multispectral imaging.

R E P O RT

RMS Annual General Meeting & Section AGMs 3 October 2024 Report by new RMS Early Career Committee Chair, Katherine Paine

T

he RMS Annual General Meetings took place on Wednesday 3rd October 2024, as part of Microscopy: Advances, Innovation, Impact 2024. This was a great opportunity for each of the Science Section Chairs to give updates on their communities and welcome new members. I attended as a member of the Early Career Committee, and will now be taking over duties as chair from Liam Rooney. Liam has been a brilliant chair and contributed so much to the early career imaging community. He has been a member of the committee since it started in 2019 and has shaped it into a welcoming and dynamic committee. Our committee is enthusiastic about providing resources for early career researchers to get the most out of the RMS, including opportunities to attend or present at our mini symposium that is attached to mmc2025, partake in the Early Career Award, and other workshops that the RMS offers. I am hoping I can keep up the brilliant work Liam has done going forward and I am grateful to still have him around as cochair for the next year!

We were also treated to scientific talks in between meetings. Coming from a membrane trafficking background, I particularly enjoyed Giulia Zanetti’s talk on vesicle transport. I enjoyed hearing about the ways she was using microscopy to address her biological questions. Georgina Fletcher from Bioimaging UK also spoke about her work on Equality Diversity and Inclusion (EDI).

This sparked discussion in the room about ways in which people have benefitted from privilege and how race and class intersect.

I felt this was an important discussion to have and I found it particularly interesting to hear someone speak about regional accents and the connotations attached to them in the UK.

There is a long way to go and this was just one conversation, but I think it was a necessary component of the meeting to ensure EDI is at the forefront at the RMS. The annual general meeting was also the Early Career Award final.

Katherine Paine.

29

Attendees chat during the lunch break at the RMS AGMs.

This award is organised by the Early Career Committee and aims to showcase contributions of early career researchers to the field, whether that is a scientific contribution or their work within the community. It is always interesting to hear about the work others are doing and celebrate their achievements. We had great flash presentations from the three finalists: Liam Rooney, Harshith Bachimanchi and Akaash Kumar. It was really tough judging such amazing contributions to the field. Akaash won with his talk on his work

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developing 8 channel simultaneous live imaging. He spoke about the story behind the development and, whilst listening, I couldn’t help but imagine how I could use this technology in my research and the ways in which it could benefit me!

The meeting finished with a drinks reception which was a great opportunity to catch up with others and discuss the day’s talks. I always leave these meetings feeling inspired and this occasion was no different.

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Plumbing the depths:

a close look at some microscopic sea-creatures Dr John Hutchison, Hon FRMS

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33

In a previous article (infocus 70 pp. 4 - 15) I described some amazing structures produced by single-cell amoeba known as diatoms. Their sub-microscopic, silica shells became very popular microscope specimens in the 19th Century, and a large number of carefully mounted slides survive today, some of which are keenly sought-after.

Another class of unicellular creatures occurs, foraminifera, that are found from the bottom of the deepest oceans right up to intertidal zones. They also occur as prolific micro-fossils in chalk and limestone. The huge chalk cliffs in Southern England are made up almost entirely of foraminifera shells, known as tests, which consist mainly of calcium carbonate. They are also important indicators in oil exploration, where careful study of rock cores can reveal likely oil deposits. In contrast to the microscopic diatoms, most foraminifera tests are in the range 20 to ~ 200 micrometers in size, although some, found in the deepest ocean depths and also as fossils, may be up to several cm in size. And remember, these are the homes of single-cell organisms!

Foraminifera were first ‘discovered’ about 2000 years ago! The pyramids in Gizeh, Egypt, are in part built out of a Palaeogene limestone which contains huge numbers of Nummulites gizehensis, a large, disc-shaped foraminifera species that grew up to several centimetres across.

“One extraordinary thing which I saw at the pyramids must not be omitted.

Heaps of stones from the quarries lie in front of the pyramids. Among these are found pieces which in shape resemble lentils. Some contain substances like grains half peeled. These, it is said, are the remnants of the workmen’s food converted into stone; which is not improbable”.

Although these fossils appear on the outside to be simple, disc-shaped pieces of rock, when cut as sections they reveal a remarkable internal arrangement of linked chambers, as shown in Figure 3. These chambers often contain crude oil –

Figure 1. An example of a nummulites fossil from the limestone chips at Gheza.This one is just over 2 cm in diameter.The term derives from Latin (“nummulus”, meaning “coin”) as they were thought to have been used by the Egyptians as coins.

The geographer and philosopher Strabo (64 BC AD 25), who came from Asia Minor but lived most

34

hence their value in oil exploration. In addition, the appearance of particular species in rock samples may also indicate likely oil deposits.

Now fast-forward several hundred million years, to the mid-19th Century.

of his life in Greece, wrote about these fossils,

With diatom slides gaining in popularity with

although he did not of course realise what they

Victorian microscopists who were also keen to

were. He described them as follows:

see other wonders, and as samples of foraminifera

ISSUE 76 DECEMBER 2024

Figure 2.Typical nummulites fossils showing the range of sizes. Image credit:Wilson44191_

Figure 3. Nummulite fossil viewed in cross section. Image credit: Cactusdave.

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Figure 4. Foraminifera tests from "the coast of Australia" and "North Pacific".

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Figure 5.Three examples of a single species, Pulvinicula elegans (first identified in 1826) neatly arranged in a row. Again, no indication of where they were found, nor the mounter’s name, were added.

Figure 6. Four groups of foraminifera, arranged this time as separate species, illustrating the variety of forms.

37

Figure 7. Other arrangements are more carefully planned, as shown here.

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Figure 8. Firth has selected a variety of species and arranged them carefully in a circular pattern. In this case they came from a relatively shallow (15-17 fathoms) seabed off Rathlin Island, N. Ireland.

became available, mounted specimens became popular objects for study. Unlike diatoms which are mainly transparent silica, foraminifera tests are opaque and often white. Consequently, for microscope slides they were usually mounted on black supports, for viewing with incident illumination. Many of the earliest examples simply showed random arrays of tests, often indicating only very approximately where they were found, as in Figure 4. Note that where the following illustrations show complete slides, these are all the standard RMS 3 x 1 inch in size.

In this example no attempt has been made to separate them into individual tests, or arrange them.

In other examples considerable efforts were made to arrange the tests.

William Firth (of diatom fame, see infocus 70 p4) was a well-known mounter, and some of his work shows his skill in selecting and mounting a wide variety of foraminifera tests, as shown in Figures 8, 9, 11 and 12.

The historic expedition of HMS Challenger (1872 -76) explored many of the world’s oceans and produced a rich harvest of new data, as well as many hitherto unknown organisms including foraminifera, see Figure 10.

From off the coast of Japan samples were brought up from 1850 fathoms (11,100 ft.) which included many new species. Foraminifera from this location are shown in Figure 11, prepared by Firth with his characteristic skill.

Firth also displayed his skill in creating spectacular slides as shown in Figure 12. Here various Lagena species are arranged symmetrically to form an attractive pattern.

Carefully prepared thin sections of chalk and limestone also show fossilised foraminifera, as shown in Figure 13. In this slide several examples of Alveolina are visible. This variety of foraminifera are Figure 9. In this example Firth has assembled a wide variety of tests to illustrate the variety of shapes. Again, the location is indicated.

elliptical or spherical – the largest one here, shown in cross-section, being ~5 mm in length.

39

Fig 10. Collecting the material dredged from the bottom of the ocean.

Firth has assembled a wide variety of tests to illustrate the variety of shapes.

The Society’s own, direct links with the world of foraminifera are with a former President – Edward Heron-Allen, a lawyer who retired from his family’s law firm at the age of 50 and moved to Selsey where he embarked on a lengthy study of the foraminifera that abounded on the intertidal zone of its sandy beaches. An interesting character, he was originally named Heron Allen, but later called himself “HeronAllen”, perhaps to add some cachet! He was a true polymath with an astonishing range of interests, and published many books on archaeology, Buddhist philosophy, violin-making, Persian – he translated the entire Omar Kyayyam poem into English - and chiromancy (palmistry). He also wrote a book on how to grow good asparagus! Along with Arthur Earland he published numerous papers in the Journal of the Royal Microscopical Society (now the Journal of Microscopy) as in 1915 p 547; 1917 pp 1 – 104 and 1930 pp 359-365. He was elected President of the RMS in 1916, followed by Fellowship of the

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Figure 11. Foraminifera from the Challenger Expedition.

Figure 12.Various species of the Lagena genus, arranged symmetrically.

Figure 13.Thin section of chalk from near Trieste.

41

Figure 14. Illustration of some of Heron-Allen’s foraminifera published in our Journal in 1930.

Figure 16. “Christmas greetings” slides from 1909 and 1912, now in the Natural History Museum.

Royal Society two years later in recognition of his seminal work on foraminifera.

Figure 15. Edward Heron-Allen’s work is still recognised by a Blue Plaque and also by the Eward Heron-Allen Society – a group of enthusiasts who still hold regular symposia where they discuss some of the more esoteric aspects of his work.

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He and Earland identified and classified huge numbers of different species, showing the wide range of shapes and sizes.

a)

b)

arranged slides in the early 20th century, now held in the Museum of Wales, Cardiff. Although he donated much of his collection to the museum, they note that:

Figure 17. Examples of Ernest Heath’s work, now in the Museum of Wales. a) Slide prepared in 1908 and b) details of an elaborate arrangement.

“We don’t know much about him, apart from that he was a fellow of the Royal Microscopical Society, somehow got hold of deepsea mud from around the world, and must have had a lot of time on his hands!”

He was a Fellow in 1909, and most of his output was from that period.

Heron-Allen - perhaps surprisingly – did have a sense of fun, and rather than send Christmas

Just like the diatom slides in my previous article

greeting cards to his friends, his collaborator Arthur

(infocus 70) these foraminifera tests provide a

Earland often made slides for him containing

wonderful window into the past, attesting to the

“seasonal” arrangements of foraminifera as shown

considerable skills, insatiable curiosities and perhaps

in Figure 16.

even the eccentricities of those who created them.

The letters and numbers in these arrangements are

Some of these beautiful objects are highly sought-

made of foraminifera tests. The particular species that lived in these tubes, having ‘selected’ fine sand grains and glued them together to form tubules of varying lengths and curvatures in which they could live safe from predators.

One of our early Fellows, Ernest Heath,(1860 – 1942)

also produced a wonderful collection of

after collectors’ items, and it is not difficult to understand why. Looking down the microscope more than 100 years after their creation, I suspect the sense of wonder for today’s viewers remains every bit as powerful.

Dr John Hutchison, Hon FRMS

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Journal of

Microscopy The Journal of Microscopy publishes top quality research articles, review articles and Hot Topic papers covering all aspects of microscopy and analysis.

This includes cutting-edge technology and innovative applications in physics, chemistry, material and biological sciences.

You can read the latest Early View papers online at www.journalofmicroscopy.org They include:

ORIGINAL ARTICLE

Imaging and observation of microcirculation in bowel mucosa using sidestream dark field imaging Keming Jiang, Lihong Chen, Hengyu Zhao, Huanxin Hu, Sicong Lai, Xinzhe Zhao, Hongda Zhang, Jia Ke, Qiongyu Hu Sidestream dark field (SDF) imaging is a tool for assessing microcirculation, commonly used for early diagnosis and monitoring of sepsis. In this study, we used SDF imaging to observe and assess the microcirculation of the intestinal mucosa during bowel surgery. We also compared different performance between normal mucosa and diseased mucosa using SDF imaging. SDF imaging was conducted in 13 patients to evaluate microcirculation parameters.

All patients were assessed at distances of 0, 1, 2, 3 and 4 centimeters (cm) from the edge of the mesentery, respectively. Microcirculatory parameters such as microvascular flow index (MFI), proportion of perfused vessels (PPV), vascular density (VD), total vessel density (TVD), perfused vessel density (PVD) and heterogeneity index (HI) were measured in these patients. Compared to normal intestinal mucosa, the diseased intestinal mucosa exhibited higher values for VD (p = 0.044), TVD (p = 0.006) and PVD (p = 0.007). No significant differences in PPV, MFI and HI were observed between the two groups. The microcirculation parameters (MFI, PPV and PVD) of the intestine at the distal distance of

3 cm were significantly lower than those at a distance of 2 cm (MFI 1.5 (0.75) vs. 3 (0.5), PPV 57.6 (9.1) vs. 97.1 (8.6)% and PVD 11.395 (3.082) vs. 20.726 (4.115) mm/mm2). In conclusion, SDF imaging is an advanced technique that provide real-time visualization of intestinal mucosal microcirculation. It has the potential to assess the blood perfusion of the intestine during surgery.

ORIGINAL ARTICLE - Open access In situ isotropic 3D imaging of vasculature perfusion specimens using x-ray microscopic dual-energy CT Stephan Handschuh, Ursula Reichart, Stefan Kummer, Martin Glösmann Microscopic 3D imaging of the vasculature of laboratory animal models such as the mouse can help to identify and understand vascular disorders.

Microscopic x-ray computed tomography is one of the most widely used imaging techniques for this purpose. High-resolution insights are typically gained from the tissues of dead animals, where an x-ray dense contrast agent was postmortem supplied to the

45

bloodstream. This work presents sample preparation and imaging protocols that allow to depict and analyse microvasculature in the structural context of mineralised (bone and teeth) and non-mineralised (e.g. brain) tissues, thus expanding the toolkit for the quantitative analyses of vascular morphology.

METHODS AND PROTOCOLS Open access Innovative sample preparation using alcohol dehydration and high refractive index medium enables acquisition of two-channel superresolution 3D STED image of an entire oocyte Michaela Frolikova, Michaela Blazikova, Martin Capek, Helena Chmelova, Jan Valecka,Veronika Kolackova, Eliska Valaskova, Martin Gregor, Katerina Komrskova, Ondrej Horvath, Ivan Novotny Super-resolution (SR) microscopy is a cuttingedge method that can provide detailed structural information with high resolution. However, the thickness of the specimen has been a major limitation for SR methods, and large biological structures have posed a challenge. To overcome this, the key step is to optimise sample preparation to ensure optical homogeneity and clarity, which can enhance the capabilities of SR methods for the acquisition of thicker structures.

Oocytes are the largest cells in the mammalian body and are crucial objects in reproductive biology. They are especially useful for studying membrane proteins.

However, oocytes are extremely fragile and sensitive to mechanical manipulation and osmotic shocks, making sample preparation a critical and challenging step.

We present an innovative, simple and sensitive approach to oocyte sample preparation for 3D STED acquisition. This involves alcohol dehydration and mounting into a high refractive index medium.

This extended preparation procedure allowed us to successfully obtain a unique two-channel 3D STED SR image of an entire mouse oocyte. By optimising

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sample preparation, it is possible to overcome current limitations of SR methods and obtain high-resolution images of large biological structures, such as oocytes, in order to study fundamental biological processes.

Lay Abstract: Super-resolution (SR) microscopy is a cutting-edge tool that allows scientists to view incredibly fine details in biological samples. However, it struggles with larger, thicker specimens, as they need to be optically clear and uniform for the best imaging results. In this study, we refined the sample preparation process to make it more suitable for SR microscopy. Our method includes carefully dehydrating biological samples with alcohol and then transferring them into a mounting medium that enhances optical clarity.This improved protocol enables high-resolution imaging of thick biological structures, which was previously challenging. By optimizing this preparation method, we hope to expand the use of SR microscopy for studying large biological samples, helping scientists better understand complex biological structures.

RAPID PUBLICATION Electron microscopy of seismic waves Shaoqing Chen, Mengyao Wang, Dong Sheng He Changes in the surrounding environment,if transmitted to the electron microscope, are frequently perceived as noise that diminishes the quality of the images.

However, in fact, ‘noises’ contain rich information about the environment.This work reports a very rare event where aberration-corrected HAADF-STEM images were acquired during the impact of seismic waves, resulted from a mild earthquake. By analysing these images, we found that the drift and vibration of the sample are detectable and quantifiable. Despite many potential challenges, this work demonstrates the utilisation of electron microscopes in detecting and monitoring seismic waves with high spatial resolution, which may lead to unique applications in the low-frequency regime.

ORIGINAL ARTICLE Neural network-assisted localization of clustered point spread functions in single-molecule localization microscopy Pranjal Choudhury, Bosanta R. Boruah Single-molecule localization microscopy (SMLM), which has revolutionized nanoscale imaging, faces challenges in densely labelled samples due to fluorophore clustering, leading to compromised localization accuracy. In this paper, we propose a novel convolutional neural network (CNN)-assisted approach to address the issue of locating the clustered fluorophores. Our CNN is trained on a diverse data set of simulated SMLM images where it learns to predict point spread function (PSF) locations by generating Gaussian blobs as output. Through rigorous evaluation, we demonstrate significant improvements in PSF localization accuracy, especially in densely labelled samples where traditional methods struggle. In addition, we employ blob detection as a post-processing technique to refine the predicted PSF locations and enhance localization precision. Our study underscores the efficacy of CNN in addressing clustering challenges in SMLM, thereby advancing spatial resolution and enabling deeper insights into complex biological structures.

ORIGINAL ARTICLE - Open Access LiveLattice: Real-time visualisation of tilted light-sheet microscopy data using a memory-efficient transformation algorithm Zichen Wang, Hiroyuki Hakozaki, Gillian McMahon, Marta Medina-Carbonero, Johannes Schöneberg Light-sheet fluorescence microscopy (LSFM), a prominent fluorescence microscopy technique, offers enhanced temporal resolution for imaging biological samples in four dimensions (4D; x, y, z, time). Some of the most recent implementations, including inverted selective plane illumination microscopy (iSPIM)

and lattice light-sheet microscopy (LLSM), move the sample substrate at an oblique angle relative to the detection objective’s optical axis. Data from such tilted-sample-scan LSFMs require subsequent deskewing and rotation for proper visualisation and analysis. Such data preprocessing operations currently demand substantial memory allocation and pose significant computational challenges for large 4D dataset. The consequence is prolonged data preprocessing time compared to data acquisition time, which limits the ability for live-viewing the data as it is being captured by the microscope. To enable the fast preprocessing of large light-sheet microscopy datasets without significant hardware demand, we have developed WH-Transform, a memory-efficient transformation algorithm for deskewing and rotating the raw dataset, significantly reducing memory usage and the run time by more than 10-fold for large image stacks. Benchmarked against the conventional method and existing software, our approach demonstrates linear runtime compared to the cubic and quadratic runtime of the other approaches. Preprocessing a raw 3D volume of 2 GB (512 × 1536 × 600 pixels) can be accomplished in 3 s using a GPU with 24 GB of memory on a single workstation.Applied to 4D LLSM datasets of human hepatocytes, lung organoid tissue and brain organoid tissue, our method provided rapid and accurate preprocessing within seconds.

Importantly, such preprocessing speeds now allow visualisation of the raw microscope data stream in real time, significantly improving the usability of LLSM in biology. In summary, this advancement holds transformative potential for light-sheet microscopy, enabling real-time, on-the-fly data preprocessing, visualisation, and analysis on standard workstations, thereby revolutionising biological imaging applications for LLSM and similar microscopes.

ORIGINAL ARTICLE - Open Access Geometric characteristics of stromal collagen fibres in breast cancer using differential interference contrast microscopy Suzan F. Ghannam, Catrin Sian Rutland, Cinzia

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Allegrucci, Melissa L. Mather, Mansour Alsaleem, Thomas D. Bateman-Price, Rodhan Patke, Graham Ball, Nigel P. Mongan, Emad Rakha Breast cancer (BC) is characterised by a high level of heterogeneity, which is influenced by the interaction of neoplastic cells with the tumour microenvironment.

The diagnostic and prognostic role of the tumour stroma in BC remains to be defined. Differential interference contrast (DIC) microscopy is a label-free imaging technique well suited to visualise weak optical phase objects such as cells and tissue.This study aims to compare stromal collagen fibre characteristics between in situ and invasive breast tumours using DIC microscopy and investigate the prognostic value of collagen parameters in BC. A tissue microarray was generated from 200 cases, comprising ductal carcinoma in situ (DCIS; n = 100) and invasive tumours (n = 100) with an extra 50 (25 invasive BC and 25 DCIS) cases for validation was utilised. Two sections per case were used: one stained with haematoxylin and eosin (H&E) stain for histological review and one unstained for examination using DIC microscopy.

Collagen fibre parameters including orientation angle, fibre alignment, fibre density, fibre width, fibre length and fibre straightness were measured.

Collagen fibre density was higher in the stroma of invasive BC (161.68 ± 11.2 fibre/µm2) compared to DCIS (p < 0.0001). The collagen fibres were thinner (13.78 ± 1.08 µm), straighter (0.96 ± 0.006, on a scale of 0–1), more disorganised (95.07° ± 11.39°) and less aligned (0.20 ± 0.09, on a 0–1 scale) in the invasive BC compared to DCIS (all p < 0.0001). A model considering these features was developed that could distinguish between DCIS and invasive tumours with 94% accuracy. There were strong correlations between fibre characteristics and clinicopathological parameters in both groups. A statistically significant association between fibre characteristics and patients’

outcomes (breast cancer specific survival, and recurrence free survival) was observed in the invasive group but not in DCIS. Although invasive BC and DCIS were both associated with stromal reaction, the structural features of collagen fibres were significantly different in the two disease stages. Analysis of the stroma fibre characteristics in the preoperative core biopsy specimen may help to differentiate pure DCIS from those associated with invasion.

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Submit online at https://mc.manuscriptcentral.com/jmi View the Guidelines for Authors and full submission details online at:

www.journalofmicroscopy.org 48

ISSUE 76 DECEMBER 2024

Journal of Microscopy News Imaging ONEWORLD: New call for papers for JoM Special Issue!

Second volume of popular Special Issue to be titled ‘Microscopy at a Glance’ The Journal of Microscopy is pleased to announce a ‘Call for Papers’ for a second volume of the recently

published

Imaging

ONEWORLD

poster special issue.

The second volume of poster articles, to be titled ‘Microscopy at a Glance’, will be guest edited by Kirti Prakash, Carlas Smith, Fei Xia, Nabanita Chatterjee, and Christian Franke.

It follows the success of the first volume, which featured a diverse range of articles by speakers from the Imaging ONEWORLD talks series which was held between 2020-2023.

We are now welcoming poster articles for the

The first volume of the Imaging ONEWORLD poster special issue was published in November.

second volume. The deadline for submissions is 30

Find out more, including submission

June 2025.

guidelines

New special issue in the Journal of Microscopy from the RMS Data Analysis in Imaging committee!

We are pleased to announce the publication of a

The idea for the issue came from discussions

new special issue (December 2024) which features

at the RMS Data Analysis in Imaging science

papers on the theme of Data Analysis in Imaging.

section meetings. In the introduction to the special

The special issue was guest edited by Rocco

issue, Rocco, Laura and Chas write: “Image data

D’Antuono (The Francis Crick Institute and

analysis is essential across many fields of scientific

University of Reading, UK), Laura Murphy (University

research. A thorough knowledge of different

of Edinburgh, UK) and Chas Nelson (Fjelltopp, UK).

methods and software tools is critical for the

49

success of many research projects.

CellProfiler plugins – An easy image

“The availability and reproducibility of workflows,

analysis platform integration for

familiarity with state-of-the-art algorithms, and

containers and Python tools Erin Weisbart,

appropriate training are vital for researchers who

Callum Tromans-Coia, Barbara Diaz-Rohrer, David

need to employ data analysis in imaging.

R. Stirling, Fernanda Garcia-Fossa, Rebecca A. Senft,

“With these community needs in mind, in 2018,

Mark C. Hiner, Marcelo B. de Jesus, Kevin W. Eliceiri,

Dominic Waithe started the efforts to build a

Beth A. Cimini

community of scientists working in this field. This developed into an RMS Image Analysis Focused Interest Group in 2018 before graduating to become the ‘Data Analysis in Imaging’ (DAIM) RMS Science Section in 2021.

“Once established, we launched an open call to the community for papers with a focus on tools and workflows for image analysis and image data management.” (‘Data analysis in imaging (DAIM) – A new RMS science section’ Rocco D’Antuono, Laura Murphy, Chas Nelson, https://doi.org/10.1111/ jmi.13366) The issue features the following papers: ModularImageAnalysis (MIA): Assembly

Cover image shows:

of modularised image and object analysis

• Fluorescence microscopy image and cell nuclei

workflows in ImageJ Stephen J. Cross, Jordan

labelled with MIA software for modular image

D. J. R. Fisher, Mark A. Jepson

analysis [Cross, Fisher, and Jepson, 2023].

Comparison of the SMLM technique and

the

confocal resolved

algorithm

microscopy

for

super-

localisation microscopy [Umney et al., 2024].

cellulose

fibres

• Mean-Shift Super-Resolution (MSSR) applied

Josué David Hernández-Varela, Susana Dianey

of

to analyse images of biomaterials [Hernández-

Gallegos-Cerda, José Jorge Chanona-Pérez, Liliana

Varela et al., 2024].

Edith Rojas Candelas, Eduardo Martínez-Mercado

• Wordcloud of searched topics on image.sc that

Bridging

imaging

users

to

imaging

led to the implementation of CellProfiler plugins

analysis

–

community

survey

[Weisbart et al., 2024].

A

Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini Annotation and automated segmentation of

single-molecule

localisation

microscopy data Oliver Umney, Joanna Leng, Gianluca Canettieri, Natalia A. Riobo-Del Galdo, Hayley Slaney, Philip Quirke, Michelle Peckham, Alistair Curd

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with deep learning models for single molecule

MSSR

imaging

in

• Cell membrane receptors automatically analysed

ISSUE 76 DECEMBER 2024

• Pie chart of the roles of the respondents to the joint COBA, BINA, and RMS-DAIM survey on biomedical and physical imaging community [Sivagurunathan et al., 2023].

• The armadillo is the adopted logo of the Data Analysis in IMaging (DAIM) RMS section.

• Cover created by: Rocco D’Antuono (The Francis Crick Institute)

Submit to infocus infocus welcomes submissions of articles of general interest to microscopists.

You provide the text and images and we take care of the rest. It’s the ideal way to share your work with the microscopical community.

Full submission information and guidelines are available at www.infocus.org.uk.

To submit an idea or if you have any questions about the process please email the Editor (editor@infocus.org.uk)

2024 Scientific Achievement Award-winners announced!

Outstanding mid-career researchers receive recognition for their work

T

he RMS is delighted to reveal the winners of its 2024 RMS Scientific Achievement Awards. Open to applicants worldwide, the award celebrates outstanding scientific achievements in any area of microscopy or flow cytometry for established mid-career researchers.

RMS President Dr Peter O’Toole said: “It is a real privilege to announce these awards and to give richly deserved recognition to some of the leading scientists currently working within microscopy.

Our winners have all made immense and sustained contributions within their fields over many years, as a great number of people within the microscopy community will know. My warmest congratulations go to them all.”

The winners of this year’s Scientific Achievement Awards are as follows: Dr Justin W. Taraska National Heart, Lung, & Blood Institute, National Institutes of Health (NHLBI, NIH) Justin is a leading cellular biophysicist and microscopist who specialises in imaging the molecular structure of cells with advanced light and electron microscopy.

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ISSUE 76 DECEMBER 2024

He has dedicated his research career to filling a fundamental gap in our understanding of how proteins assemble multi-component complexes at the nanoscale inside living cells.

Justin has focused the majority of his attention on organelle trafficking, where he has been a true

innovator and leader in the field for nearly 20 years.

His lab at the NIH has developed many new imaging and analysis tools for quantitative live cell, superresolution, electron, cryogenic, and correlative light and electron microscopy.

The overall impact of Justin’s work emerges from his keen ability to identify key biological questions and address them through the development of new microscopy tools. This fusion of question and technology has resulted in progress in visualizing healthy and diseased cells in ways not previously possible.

By pushing the boundaries of microscopy and cellular biophysics, Justin is uncovering the architecture of the cell at the nanoscale. The approaches developed in his lab are applicable to a wide range of biological questions and systems and his impact goes well beyond the trafficking field.

His work is always at the cutting edge, driving a new era of understanding how cells work.

Professor Roland Kröger University of York

Roland’s impressive interdisciplinary research has broken new ground in applying transmission electron microscopy and spectroscopy techniques to the study of nanomaterials, electronic materials, soft materials and unique bio/materials - truly bridging both the life and materials sciences.

He has achieved great success through bringing advanced materials physics techniques into a range of different fields such as biology, archaeology and environment. His contributions to elucidating the 3D nanoscale organisation of bone has found strong resonance and help to pave the way for a full understanding of bone formation, a field of great significance in biomedical sciences.

Roland’s liquid phase microscopy research using novel in situ platforms permit the real-time assessment of dynamic reactions in liquid environments. His establishment of in situ characterisation methods at York extend beyond transmission electron microscopy and include multi-technique methods,

combining TEM with in situ Raman microscopy in order to explore the behaviour of biomaterials under challenging complex environments combining liquid and stress.

Roland has been the major TEM/STEM collaborator in significant interdisciplinary programs and scientific publications that have explored bone structure and properties, which have led to a range of unique research collaborations on bone diseases, studies of new bone-like materials, and mineralised tissue regeneration. He is now working with NHS Hospitals in York and Scarborough on the potential role of microcalcification in wound healing.

Roland has also been extremely active in the Royal Microscopical Society for many years, where he has also championed interdisciplinary materials research activities, particularly in non-traditional areas.

Dr Bernd Gotsmann IBM Research GmbH

Bernd is a prolific contemporary scientist working in scanning probe microscopy (SPM), expanding it way beyond the nanoscale topographical imaging the original STM provided.

His research has uncovered unique SPM benefits that neither light nor electron microscopies can provide, namely - direct imaging, measurements, and manipulation of nanoscale physical properties of studied objects.

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She has a strong background in programming, data analysis and maths, which has enabled her to develop a number of exciting new methods. She uses her microscopy and programming expertise to work with other groups to apply these new methods and make new discoveries in cell biology.

Throughout his career, Bernd has demonstrated unparalleled dedication and innovation in advancing our understanding of nano-thermal properties through the development and application of cuttingedge scanning probe techniques. His contributions have significantly enriched the field, paving the way for groundbreaking discoveries and advancements in nanoscience and nanotechnology.

Bernd’s expertise and leadership in nano-thermal characterisation have been instrumental in addressing fundamental questions and challenges in various scientific disciplines, including materials science, physics, and engineering. His pioneering research has not only expanded our theoretical knowledge but has also led to practical applications with profound implications for technology development and industry.

In addition to his remarkable scientific achievements, Bernd is widely respected for his mentorship and collaboration within the scientific community. His passion for knowledge sharing and his commitment to fostering the next generation of scientists make him an invaluable asset to the field of microscopy and beyond.

Dr Susan Cox

King’s College London Susan has an international reputation as an expert in the analysis of single molecule light microscopy data to create super-resolution images.

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ISSUE 76 DECEMBER 2024

Her position in the field can be seen from both her publications and a high number of invited talks, including talks within the last few years at Focus on Microscopy, Methods and Applications in Fluorescence, and the American Society for Cell Biology - all major international meetings. Her work has been recognised with the RMS Light Microscopy medal, the SEB President’s medal, and the Howard Lecture.

Her paper output is impressive, including final author papers in Nature Methods, Nature Communications, and the European Journal of Cell Biology.The Nature journal papers are both based around achieving accurate and reproducible results in super-resolution imaging, a field in which she is now one of a small number of internationally recognised experts.

Susan has recently been focusing on cell interactions with matrices, and the big data, deep learning approaches required to enable these studies, while maintaining her single molecule standards research.

This approach is likely to produce a substantial amount of high-impact work, and to prove highly beneficial to microscopists and cell biologists worldwide.

R E P O RT

Latin America Bioimaging Meeting and LABIxSuperres Rio de Janeiro, Brazil 18 – 23 August 2024

D

uring the week of 18-23 August 2024, I participated in the Latin America Bioimaging (LABI) Meeting in Rio de Janeiro (Brazil). I presented our new initiative, Global BioImage Analysts’ Society (GloBIAS), as well as contributing to “LABIxSuperres” – a workshop on super-resolution microscopy, reporting on our software suite of computational methods for super-resolution.

These initiatives allowed the exchange of expertise between more than 100 scientists from Latin America, who work as facility staff or use advanced bioimaging for their research.

LABI (https://labi.lat/) is the network that aims to improve education and training on bioimaging in Latin America and the Caribbean. Moreover, it aims to facilitate access to the latest technologies for the scientists in the region.

The LABI meeting began with Program Coordinator Andrés Olivera introducing the activities and opportunities for training and career development available to all members.This was followed by Imaging 4 All (i4A) project manager, Deniz Saltukoglu, who announced the funding opportunities for Imaging Scientists provided by Global BioImaging.

As co-PI and steering committee member, I presented the initiatives of the Global BioImage Analysts’ Society (GloBIAS) for networking, training, and education

of bioimage analysts around the world. GloBIAS is supported by a grant of the Chan Zuckerberg Initiative, to become a self-sustaining scientific society that allows knowledge exchange between members, develops a curriculum for bioImage analysts, creates and maintains repositories for training materials, and consolidates standards for bioimage analysis.

During the networking session I learned about the activities of the different LABI Working Groups and took part in discussions on the common needs of imaging scientists and how to transform needs into actionable ideas, and finally into results. Some useful insights offered by the LABI include its focus on governance and sustainability of the network, by assuring co-leadership for a smooth transition

(Left) Rocco D’Antuono presenting the Global Bioimage Analysts’ Society at the Latin America Bioimaging Meeting. Middle) Prof. Kildare Miranda, local organiser of LABI Meeting 2024, leading the visit to Advanced Microscopy Unit at the CENABIO. Right) Jessica Marques, Aldenora Vasconcelos and Jander Guimarães, from University of the State of Amazonas (UEA), meeting local school students during the LABI outreach activity.

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Participants of the Latin America Bioimaging Meeting and LABIxSuperres – Rio de Janeiro, Brazil, 18-23 August 2024, Photo credit: https://x.com/ LatamBioimaging/status/1826693086161842567/photo/1

between chairs, and the profound involvement of the community, with the goal of improving the sense of belonging to the LABI network.

One session that I particularly enjoyed was titled “Exploring Open Science in Bioimaging”, during which examples of successful labs championing the use of open source software and hardware were showcased, such as the presentation of the Latin American Hub for Bioimaging Through Open Hardware (LIBRE Hub) in Chile, led by Tobias Wenzel.

As a great way to end the meeting, we visited the core facilities at the National Center for Structural Biology and Bioimaging (CENABIO), hosted by the local organisers. Finally, the LABI meeting included the involvement of bioimaging researchers in the outreach activity at Jardim Botânico (Botanical Garden), where we could all speak to local school students to explain our job in science, and perhaps motivate them to become researchers.

The second part of the week was dedicated to the LABIxSuperres meeting, which started with the report of the Fluorescence Nanoscopy in Bioimaging Foundational Project, aimed at Expanding Global Access to Biomaging in Latin America (presented by Mariano Buffone, IBYME, Argentina).

A history lesson covering 10 years of super-resolution microscopy, held by Adán Guerrero (UNAM, Mexico), set the scene for the following showcase of applications of super-resolution microscopy in Latin America, including single molecule imaging, STED, SMLM, and computational methods.

I had the opportunity and honour to contribute to the session “Expanding worldwide access to Super Resolution Microscopy”, which included a plenary talk on pioneering open-source AI technologies, presented

by Ricardo Henriques (IGC, Portugal) and another plenary talk on democracy in microscopy with

affordable fluorescence microscopes, presented by Ali Shaib (Universitätsmedizin Göttingen, Germany).

In my talk, I reported on the progress in developing napari-superres, a suite of computational methods for super-resolution microscopy based on fluorescence fluctuations, a collaboration with the group of Adán Guerrero, at the National Laboratory for Advanced Microscopy (UNAM, Cuernavaca, Mexico).

The LABI Meeting and LABIxSuperres 2024 delivered valuable lessons in bioimaging, physics, facility management, and biological projects, but beyond that, there were some great moments of unscheduled scientific discussions and networking, while riding on the bus or dining out. I would certainly make the case for choosing in-person meetings, when possible, and fully engaging with the community without the distraction of emails or other virtual calls. The hybrid way of running conferences does have the potential to bring a wider group together, but in my view, it can reduce focus, and limit the capacity for in-depth brainstorming.

Such engaging meetings are not possible without the efforts of organisers, supporting staff and students, attentive funders, and the commitment of the community members. Therefore, it’s imperative to mention at least one representative of each category: as a speaker and participant, thank you to Kildare Miranda, Andrés Olivera, Lía Pietrasanta, Adán Guerrero, Haydee Hernández, Celina Terán, Vladimir Ghukasyan, Jander Guimarães, to name a few.

I would like to thank the Royal Microscopical Society, GloBIAS and the LABI network for the support to attend these meetings, allowing me to interact with all the great Latin American scientists.

Rocco D’Antuono FRMS, Principal Microscopist and Image Analyst, Crick Advanced Light Microscopy STP, The Francis Crick Institute, London, UK

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A new web resource for diatom optical microscopy www.diatomimaging.com Dr Jonathan Crowther, FRMS

When I started on my journey into microscopy in 2020, the initial aim was to make a UV transmission microscope for my research into sunscreens (previously written about in Crowther, 2021). Very soon I found myself in need of something to help me determine the resolution of my microscope and this was where I was introduced to the wonderful world of diatoms. For those of you who are not familiar with these little marvels, diatoms are algae that produce silica structures to live in. Some species are currently alive, and others are present in fossil deposits. The silica structures are amazingly intricate and come in a myriad of shapes and sizes with structures present in the micron and nanometer scale. For my UV work, I approached a couple of slide makers, and after supplying them with fused silica slides and coverslips, had some diatom slides made which I used to help with development and testing of my microscope (Crowther, 2022).

58

Diatoms have been a subject for microscopy since

by bit the number of slides grew. All the while I

the 1800s and a huge range of slide makers had

was capturing images and gradually refining my

produced slides with them on. Some of these slides

technique, and as a result was building up a large

are strews (with a scattering of different material

collection of high resolution images. After sharing

from a location), some were examples of selected

these images online (usually through the Diatom

diatoms, and some were amazing arrangements

Images Facebook Group) a number of people had

of tens or even hundreds of individual diatoms. I

asked me what I was going to do with the photos.

became fascinated by their widely varying structures

Initially I thought about a photobook, but then

and started to obtain slides to image. Soon I found

decided to create a website where I could share

myself looking out for specific makers and certain

them, along with photos of the slide and details on

species to try and build my collection, and bit

how the images were captured.

ISSUE 76 DECEMBER 2024

20μm

Figure 1. Arachnoidiscus ornatus by Mike Samworth. From Santa Ana, California. Olympus BHB microscope using 450nm LED light. 63x Leitz Pl Apo NA 1.40 objective, oil immersion. Olympus Aplanat Achromat condenser, oil immersion, slightly oblique lighting. Image provided by Dr Jonathan Crowther FRMS, JMC Scientific Consulting Ltd (https://diatomimaging.com/).

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20μm

Figure 2. Auliscus stöckhardtii by WA Firth. From Allan’s Farm, Oamaru.

Olympus BHB microscope using 450nm LED light. 63x Leitz Pl Apo NA 1.40 objective, oil immersion. Olympus Aplanat Achromat condenser, oil immersion, oblique lighting. Image provided by Dr Jonathan Crowther FRMS, JMC Scientific Consulting Ltd (https://diatomimaging.com/).

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20μm

Figure 3.Triceratium morlandii by Klaus Kemp. From Oamaru, New Zealand. Accepted name Entogoniopsis morlandii. Olympus BHB microscope using 450nm LED light. 40x Leitz Pl Apo NA 1.00, oil immersion. Olympus Aplanat Achromat condenser, oil immersion, brightfield lighting. Image provided by Dr Jonathan Crowther FRMS, JMC Scientific Consulting Ltd (https://diatomimaging.com/).

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0.5mm

Figure 4. Large arrangement from St Peter’s, Hungary, by Watson and Sons Ltd. Olympus BHB microscope using white LED light. 3.2x Zeiss Semiplan NA 0.10 objective with no substage condenser lens. Image provided by Dr Jonathan Crowther FRMS, JMC Scientific Consulting Ltd (https://diatomimaging.com/).

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The site (www.diatomimaging.com) was launched

of which have been converted to monochrome

earlier this year. At the time of writing this article,

primarily for my UV work. Image stacking is done

it has around 400 images on it and I am regularly

in Zerene, and I move the stage manually to collect

adding more content.

the images for these stacks. One thing I wanted to

The goal with the site was to create an online museum, where images of the diatoms themselves could be viewed in high resolution. It was important to me to show the slides as well. These are amazing

do was show what can be achieved with relatively modest equipment (although I really do recommend to invest in the best objectives you can for imaging diatoms).

creations, especially the large arrangements, and the

While the site has been developed with a scientific

makers need to be celebrated. As I am a scientist,

focus in mind, I’m sure it will be of interest to a

details on how the images were taken have also

wider audience, including those who just enjoy the

been shared, especially as I haven’t really found

wonders of nature. If nothing else I hope it will

anywhere which shared all these aspects of the slides at the same time.There are plenty of websites which show wonderful artistic representation of diatoms, but I wanted to create something more scientifically orientated. While I do not consider myself an expert in taxonomy, I try to put any new names in with the discussion, and also in the few instances where the slides are mis-named, correct that.

prompt others to share their collections as well.

There must be many slides in people’s collections which would be useful for the world of research if they could be made available. I am always on the lookout for slides to image, so if you have ones available which you are looking for a new home for, please feel free to contact me.

References “UV transmission microscopy – optical imaging

For imaging I tend to use fairly basic techniques

without

– brightfield and oblique lighting, along with

magazine (Royal Microscopical Society), 2021, 64,

occasionally using dark ground. I often use a

4-15.

homemade 450nm LED light for illumination as the

“Ultraviolet imaging of diatoms”, Jonathan Crowther,

short wavelength helps with optimising resolution.

Quekett Journal of Microscopy, 2022, 44, 273-284.

The microscope is an Olympus BHB from the 1970s

glass”, Jonathan

Crowther

infocus

or 80s. For objectives my ‘go to’ ones are 4x, 10x

Dr Jonathan Crowther, FRMS

and 20x Nikon Plan Apo, along with 40x, 63x and

JMC Scientific Consulting Ltd

100x Leitz Pl Apo ones which are oil immersion.

Email: jonathan@jmcscientificconsulting.com

The cameras are SLR or mirrorless, a couple

Website address : https://diatomimaging.com/

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New Member Welcome The Royal Microscopical Society would like to welcome our new members who have joined us in the last three months. We hope they enjoy a long and rewarding membership with the RMS. Mr Ian Cardillo-Zallo Jake Richardson Mr Jonathan Amara Dr Hongyu Wang Innes Clatworthy Mr Arkapravo Das Dr Cristina Martínez González Dr Mehrnoosh Neshatian

Mr Ross Walsh Miss Emma Westlund Dr Merve Açikel Elmas Ms Vasiliki Tsioligka Miss Emilia Coward Miss Laura Davidson Dr Maciej Trzaskowski Mr Jan Majer

Miss Emma Long Mr Pasindu Eranga Raigama Arachchige Dr Dongsheng He Ms Sara Salgueiro Torres Dr Inna Goliand Dr Iestyn Pope

If you know of anyone who might be interested in becoming a member of the Royal Microscopical Society and if you would like us to contact them, please send their details to our Membership Administrator, Debbie Hunt – debbie@rms.org.uk Application forms are available to download at www.rms.org.uk/membership Don't forget you can now log into the RMS website and check your membership status, renew and download receipts. If you have never logged into the RMS website, please enter the email address that is linked to your membership and then click 'forgotten password'.

If you have any queries or questions about your membership please contact Debbie Hunt debbie@rms.org.uk

Member Profiles Name

Arkapravo Das Tell Us About You? I completed my schooling at Don Bosco School, Liluah, and am currently pursuing an undergraduate degree in Zoology (Honours) at the University of Calcutta. I am a research enthusiast and an aspiring biologist with a deep passion for learning and a dedicated approach to my studies. I am eager to contribute to the Royal Microscopical Society as an Undergraduate Member, leveraging my knowledge and skills to advance our understanding of the microscopic world.

Why did you become a member of the RMS? So that I can contribute as a member of society to the microscopic bio world. And learn a lot of things as a member. "Microscopic biology unveils

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ISSUE 76 DECEMBER 2024

the hidden architecture of life, where the smallest structures define the grandest functions."

How do you feel being an RMS member benefits you?

Becoming a member of the Royal Microscopical Society will not only provide me with valuable access to cutting-edge research, resources, and a community of experts in the field, but also allow me to contribute meaningfully.

This membership will facilitate the acquisition of knowledge and insights with ease, helping me stay updated with the latest advancements and best practices in microscopy and biological sciences. Additionally, I look forward to sharing my perspectives, participating in discussions, and contributing to the society’s initiatives, thereby supporting the collective growth and innovation within the field.

Name

Pasindu Eranga Tell Us About You? I'm an undergraduate in Zoology, with minors in Chemistry and Microbiology, focused on computational biology. I specialise in highmagnification insect photography for entomology and am interested in darkfield, metallurgical, phase contrast, and confocal microscopy, especially with large working distance objectives.

Through RMS, I aim to connect and expand my knowledge in these areas.

to engage with a diverse scientific community, attend events, and access resources aligns with my goal to stay at the forefront of microscopy advancements. I believe RMS membership will support my growth as a researcher and help me contribute to the wider scientific community.

How do you feel being an RMS member benefits you?

Joining the Royal Microscopical Society has already been a rewarding experience, opening up professional networking and learning opportunities. With an efficient registration process, I received my membership quickly, giving me access to a range of valuable resources. As an RMS member, I look forward to connecting with researchers, learning about new developments, and exploring advanced microscopy techniques that can enhance my studies and research.

Through RMS, I hope to build connections that will enrich my work in computational biology and high-magnification photography. The chance

Submit to infocus infocus welcomes submissions of articles of general interest to microscopists.

You provide the text and images and we take care of the rest. It’s the ideal way to share your work with the microscopical community.

Full submission information and guidelines are available at www.infocus.org.uk.

To submit an idea or if you have any questions about the process please email the Editor (editor@infocus.org.uk)

65

Spotlight on…

Kim Findlay In this issue we speak to Kim Findlay, Head of Bioimaging at the John Innes Centre (JIC) in Norwich, UK, as she looks ahead to her retirement – an impressive 38 years after joining the organisation.

A well-known and highly respected scientist within the microscopy community, Kim is a former RMS Council member and long-standing Ambassador for the Society. She was also awarded the inaugural RMS Vice President’s Award in 2015, for her outstanding contribution to microscopy research and laboratory support.

Her expertise is in both scanning and transmission electron microscopy and sample preparation of plant and microbial specimens for EM, especially cryo methods. Her facility at the JIC offers a wide range of services including imaging and custom sample preparation, training and technical support in a variety of microscopy techniques.

Kim’s first sense of being drawn to the world of science came on (or around) the 21st of July 1969, as she watched the iconic, grainy footage of Neil Armstrong and Edwin ‘Buzz’ Aldrin, exiting the ‘Eagle’ lunar module in slightly ungainly fashion to become the first humans to walk on the surface of the moon.

She recalls: “My first feeling was that I wanted to be an astronaut. I was so young – only four – but I can remember it vividly, being fascinated by the thought of discovering other worlds out there, and exploration that involved such an amazing amount of human ingenuity and overcoming technological challenges. At the time everybody was excited about space travel, and to bring that story to the watching public was amazing.”

While the desire to ‘boldly go’ has remained a staple of childhood dreams ever since the idea of space travel was first popularised in science fiction novels,

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ISSUE 76 DECEMBER 2024

for a young girl in the late 1960s, it was, perhaps, an unlikely aspiration.

Kim presenting her first scientific poster at the 1991 Botanical Microscopy Meeting.

Kim explains: “I

had a sister but no brother, so there was no real understanding that females were not really expected to pursue that sort of thing. Most women would not have considered technical careers but I definitely fell in love with science. I went to an all-girls school which also helped, I think, because it meant I never felt I was held back by boys – or in competition with them.”

Kim took A-Levels in maths, physics and biology, drawn to both the theoretical and experimental aspects of those subjects. Through biology, she also found an outlet for her love of nature, animals and plants. As she pondered a future career however, it was her passion for engineering and technology that came to dominate her thinking, and almost led her into a career in the air force – a similarly maledominated calling at that time.

Kim says: “I had heard that if I joined the RAF to become an officer, they would sponsor me through university – where I was thinking of doing electronic engineering - and during summer vacations, students got an opportunity to go flying. But when I went to the interview and said I wanted to sign up for a 20 year officers’ commission, they said ‘we don’t allow women to do that.’ So I thought ‘stuff you, I’ll do something else' ”, she adds, chuckling.

Eventually, after graduating from King’s College, London with a joint degree in biology and physics, Kim was offered – and initially accepted - a job working in the university’s biophysics department at Drury Lane. But after a few days’ reflection at her family home in Norfolk – and in something of a ‘Sliding Doors’ moment - she picked up the phone to inform her would-be employers that she wouldn’t be coming back to London after all. It was the decision that set Kim on course for her long career at the John Innes Centre.

67

Kim working on the SEM.

She says: “I really enjoyed London as a student, and the job was going to involve doing TEM which I loved, but once I got home to Norfolk, I realised that living permanently in a big city like London just wasn’t for me. So I ended up without a proper job for a few months, until I saw a Research Assistant job advertised for the John Innes Centre. It involved working for Clive Lloyd on the plant cytoskeleton, in the Cell Biology department headed by Keith Roberts – who was renowned among biology students, and still is, as a co-author of the textbook Molecular Biology of the Cell."

Having secured the post, Kim quickly gained a huge amount of experience working both with TEM and light microscopy techniques including immunofluorescence. One memory which stands out from her first year, is the time she was tasked

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ISSUE 76 DECEMBER 2024

with finding a way to preserve intermediate filaments in plant cells, so they could be viewed properly through the light microscope. Previously, the group had only been able to visualise them as collapsed bundles, but Clive believed they should be a filamentous network.

“I just loved that challenge”, she says, “and one day cracking it and seeing what nobody had seen for the first time. I think everyone who enjoys microscopy loves that feeling. And that has happened several times throughout my career; it’s a wonderful feeling.”

She adds: “I thought the TEM was such an amazing instrument and I enjoyed the engineering and technical side of it and the fact it used electrons, not light – it all seemed really cool and clever. I just

thought this was an amazing machine and we could

ultramicrotomy, and service work came flooding in

see such details that we couldn’t see with anything

from lots of people across the institute.”

else.”

Kim moved sideways into this core-funded post.

“My boss, Brian Wells, retired within five years and I have been head of Bioimaging ever since then.

It has grown beyond all recognition and I have had some great people in my team throughout that time.

We are now a team of six running the facility.”

She recalls: “We had TEM, SEM and an early

Reflecting on her long career at the JIC, Kim singles

confocal, and GFP technology was only just taking

out a number of significant advances in microscopy

off. They wanted someone to help look after the

– and the challenges attached to moving with the

microscopes and be able to do microscopy for

technological times.

Within a few years, the JIC had begun moving towards a ‘core’ model and wanted a microscopist to work for all groups, rather than attached to the individual research groups.This was the early 1990s, and effectively the birth of an imaging ‘core facility’ as microscopists have come to know it today.

other people.

I

immediately

She says: “I’ve been really fortunate to have started

doing

cryo-SEM

and

been alive during so many major leaps forward

Kim receiving the RMS Vice President’s Award from Debbie Stokes in 2015.

69

in microscopy. When I started, I saw the birth of

interview, the experience was captured on camera!

confocal microscopy, GFP Technology, and they

(see p67)

were just starting to talk about high pressure freezing; now I have a high pressure freezer in the lab.”

microscopists who came up to me and I had no idea who they were, but they were important folk.

“Cryo-EM wasn’t possible then, and now we’re doing single-particle analysis with cryo-EM, as well as Volume EM, so it’s just been amazing. And of course computing has just revolutionised everything we do, providing the power to handle all these massive data sets we have to deal with now.”

They were so friendly and fully engaged in what I

“I can also remember the early days of having

She says: “The community have always been so

to develop and print film. When digital cameras

welcoming to me, and you just can’t beat mmc

became available for microscopes, everyone was

for having great opportunities to network with

initially sceptical about whether they could do as

the trade representatives and imaging scientists.

well as real film, so that was a huge revolution. And

Nowadays I take my team too, to see the company

now we even have a direct electron detector on

reps and meet new people. Everyone is so

our TEM! It’s also been very exciting to see this

welcoming and the RMS does a great job.”

massive resurgence in EM, because when I first

Kim has also been a mainstay of the RMS Botanical

started, it had kind of fallen out of favour, and

meeting series since 1991, kindly volunteering

people thought it had found its limits in biology,

to host the event last year at the JIC. It was a

but now it’s back with a vengeance. And of course

particularly poignant meeting, the first since the

there’s super-resolution microscopy - we also have

death of former RMS President, Professor Chris

that technology in the facility now. Just being able to

Hawes, a key figure in the history of the event.

break the diffraction limit has been mind-boggling. I never believed when I first started here that I was going to see all these incredible things.”

was talking about, and I thought – ‘I love this’! I saw that the imaging community was just such a friendly and open community.”

Kim soon became a regular at a number of different RMS events – both as an attendee and as an invited speaker. Her first ‘Microscience’ (now the mmc series) meeting was in 1994 at Earls Court and she has been a regular fixture at the event ever since.

She says: “It was a real honour to be asked to organise it, and also to write the introduction to the Special Issue of the Journal of Microscopy to come

She adds: “There have been so many revolutions

out from that meeting. Chris was such a significant

and advances in my time, that perhaps the biggest

figure, and so popular within the community. It was

challenge has been to keep up with it all, and to make

wonderful for everyone to be able to share their

sure you have enough equipment and knowledge to

memories.”

do all the work that needs to be done.There’s never a dull moment that’s for sure. One day I might be trying to fix a vacuum leak behind an EM, and the next, I might be giving a lecture or looking down the microscope at something for the first time.”

70

She recalls:“There were several wonderful, eminent

As a teacher, Kim has trained hundreds of people to use microscopes over the years – including on the RMS Cryo-EM Course and the EM School at Leeds. In 2014 she also helped establish a new RMS course on how to colour EM images using

Kim’s first brush with the RMS came in 1991, when

Photoshop. At the JIC she has always championed

she attended the Botanical Microscopy Meeting in

education and outreach projects – notably setting

Durham. It was the first time she had presented

up an annual schools’ microscopy day from 2008

a scientific poster, and happily for this infocus

with RMS funding support. In the late 1990s she

ISSUE 76 DECEMBER 2024

even co-presented a cell biology-themed stage

panels, my first thought is usually – ‘are you sure

show for children called ‘Cell City’, which ended up

you want me?’

reaching an international audience.

“I was the first in my family to go to university and

She explains: “It involved a mixture of live demos, video clips and microscopy, and it was so successful we decided to take it to the Edinburgh International Festival of Science.Then we took it to a science festival in Leeds and there was a talent scout looking for shows to take to the Canberra Science festival in Australia. We ended up taking it

didn’t really know what a PhD was, so I just thought ‘I‘ll go and work in a lab’. I loved being at the bench and doing practical things, and amazingly my career path has brought me to this position where I’m lucky enough to have got over 100 publications through the role that I do.”

to Canberra, Sydney, Melbourne and Adelaide. That

As Kim approaches retirement, she is as busy as

was just wonderful – putting on an event like that

ever - mentoring new staff members as well as

to educate children - and definitely a fun highlight

laying the groundwork for her successor to head

in my career.”

the Bioimaging facility. Perhaps inevitably, she

Another memorable moment for Kim came in

has become increasingly mindful of the roles and

2010, when she was invited to appear on a special

responsibilities of tomorrow’s microscopists. What

episode of Gardeners’ World, looking into the

words of wisdom, for instance, might she have for

‘science of gardening’. The show’s researchers

anyone embarking on a career such as hers?

approached Kim for her scientific expertise – but as an avid gardener and devotee of the show, she

“Never underestimate the power of seeing

had even more reason to relish the invitation.

something under the microscope for the first time”,

“I watched Gardeners’ World religiously, and then I found myself driving down to Carol Klein’s garden to do a bit of filming. They wanted someone to talk about leaf adaptations and the shape and morphology of plants and that sort thing. They had no idea that I was a gardening fiend!”

she says. “Being able to visualise something, to see

In

RMS

power they have and how responsible you must be

2015

Kim

received

the

inaugural

something with your own eyes - I think microscopy is the best of all the fields because of that. It’s all very well looking at little Eppendorf tubes and someone telling you that the little white blob at the bottom is DNA, but actually seeing it down a microscope and seeing what’s going on inside cells; you can never replace that.”

She adds: “I don’t think scientists always realise the

for her outstanding

for the younger generation. Every time you teach

contributions to electron microscopy. The citation

them something you can either turn them off or

also made reference to her extensive outreach and

you can really inspire and motivate them, so being a

education activities, and her ability to “inspire the

good teacher is really, really important.

Vice President’s Award

next generation”. Four years later she was invited to join the RMS Council, on which she served until

“Every year we take on work experience students

2023, despite (in characteristically self-deprecating

and it’s just wonderful to see their faces when they

fashion) initially questioning the appointment.

look down these high-end microscopes and they

She explains: “Sometimes when I reflect on my

can’t help but go ‘wow’. A few of them have even

career, I just can’t believe my luck. I don’t have a

written back to say the experience has inspired

PhD and I’ve always had that little bit of self-doubt

them to pursue a career in science. That’s probably

– so when I’ve been asked to sit on committees or

the most rewarding thing of all.”

71

NEWS

From the RMS President Dear Readers, It has been another busy few months since our last issue of infocus, with a host of RMS meetings, conferences and courses covering a huge range of topics in microscopy, imaging and flow cytometry.

As it happens, I’m writing on the day of our inaugural Frontiers in Physical Imaging meeting in London, focusing on recent advances and improvements in electron and X-ray microscopy, as applied in the physical sciences. This new initiative follows the success of the long-established Frontiers in BioImaging, held in Oxford earlier in November. We really appreciate the ongoing support of attendees at RMS events - despite the difficult economic circumstances affecting many of our universities at the present time. On that note, I should also mention our September Flow Course, which attracted its largest number of participants for 10 years.

It was great to meet up with friends and colleagues in London at the RMS Annual General Meetings – including the majority of our Science Section AGMs. These took place in early October as part of Microscopy: Advances, Innovation, Impact 2024, which incorporated a range of brilliant talks from some highly engaging invited speakers.

When attending our Section AGMs – which cover all branches of microscopy, data analysis and flow cytometry - I am always struck by just how much each committee is actually delivering for the microscopy community on a global scale. The event also featured

the climax of the RMS Early Career Award and a series of award presentations recognising some of the latest outstanding achievements in microscopy (see p52). Congratulations to all our recent winners.

As a society, we are very mindful of the need not only to deliver for our academic membership, but also for our corporate members. To that end, we have a highly engaged Corporate Advisory Board, and a number of developing initiatives, such as our collaborative, RMS-hosted Corporate Member Events. These webinars are making available some fantastic, free content to members and nonmembers alike.

Looking ahead to the coming year, and mmc2025 is already on the horizon! I would encourage everyone to save the dates (1-3 July) and start making plans for travel and accommodation.

Don’t forget the RMS offers support in the form of travel bursaries for early career members or those working in a support role in microscopy or cytometry. As always, mmc will have something for everyone with an interest in microscopy, imaging or flow cytometry, and is not to be missed!

Finally, as we approach the year’s end, I feel it is important to recognise the efforts and dedication of the RMS staff, volunteers and committee members who enable the Society to carry out all its activities, while embracing new ideas and ways of working along the way. Despite a swiftly changing – and challenging - environment in both academia and industry, plus all the uncertainties in the wider world at present, they somehow manage to keep delivering for the microscopy community, and it is a great credit to them all.

I would like to wish you all a very happy Christmas and new year, and look forward to seeing you in 2025.

Dr Peter O’Toole, RMS President.

Dr Peter O'Toole.

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ISSUE 76 DECEMBER 2024

Dr Mark Pickering receives RMS Chris Hawes Award for Outreach and Education Congratulations to Dr Mark Pickering, who received the 2024 Chris Hawes Outreach and Education Award at the Society’s recent AGM. A neuroscientist, microscopist and educator at the University College Dublin School of Medicine, Mark’s main area of research is focused on understanding the factors underpinning the structure and function of the nervous systems.

Alongside his research activities at UCD, public and community engagement and involvement in science are cornerstones of his work. By not only informing and engaging the broader community about science but also empowering them to become active participants in the process of science themselves, he aims to democratise the process of discovery.

to many national and international public outreach and engagement initiatives including: The Dublin Maker Festival, Skype-a-Scientist, the ‘JellyLab’ and the ‘Science by the Sea’ YouTube series.

Created in honour of the late Professor Chris Hawes, former President of the RMS, for his contributions to the Society and work on showcasing to the public the many benefits of microscopy, the RMS’ Outreach and Education Award is given annually to those seen as keen advocates for science and microscopy as a whole, and who’ve inspired people to take a keener interest in the subject.

Throughout his career Mark has actively engaged with both the scientific and lay communities. He is an eloquent advocate for the importance of Microscopy and STEM initiatives from primary to tertiary education, and beyond. He has contributed

Akaash Kumar receives RMS Early Career Award 2024 entrants – including Liam Rooney (University of Strathclyde) and Harshith Bachimanchi (University of Gothenburg).

Congratulations to Akaash Kumar of MRC Laboratory of Molecular Biology (LMB), who received the RMS Early Career Award following his winning talk at the Society’s Annual General Meeting (Microscopy: Advances, Innovation, Impact 2024) in October.

The award, which recognises the achievements of early career researchers in microscopy, image analysis or cytometry, was hotly contested on the day, with excellent talks from all three shortlisted

Akaash has been working with Emmanuel Derivery and James Manton in the LMB’s Cell Biology Division and has now begun a postdoctoral placement. His talk outlined his recent work to develop a novel, versatile imaging system capable of rapid livecell imaging of up to eight biological components simultaneously.

Akaash’s work has previously been recognised with the Ph.D. Student Award for Applied Research from the Cambridge Society for the Application of Research (CSAR) and Best Talk Awards at the Warwick-Cambridge Quantitative Cell Biology Meeting (2024) and Frontiers in Bioimaging (2022) conferences.

73

NEWS

mmc2025: Great response as exhibition space goes on sale!

The RMS would like to thank the corporate community for a fantastic response after exhibition space for mmc2025 went on sale in October.

More than 80 per cent of available space has already been snapped up by companies eager to be part of the event next summer. Sales were initially opened with an exclusive window for Corporate Members, before being opened to all companies.

and the response has been fantastic since the exhibition stands went on sale. We would like to thank the corporate community for its support and encourage all companies to book their place at what promises to be a great exhibition.”

Please contact exhibition@rms.org.uk if you have any questions or require assistance.

In total, 1,188sqm of stand space has now been sold to 64 different companies and other exhibitors.

Sales for the remaining space remain open to all companies - please refer to the updated floorplan before submitting a booking.

RMS Chief Executive Sali Davis said: “We want mmc2025 to be one of our best ever congresses,

‘Microscopist Profiles’ launched on RMS website Submit your profile and read about the roles of others in microscopy If you work in microscopy we want to hear more about your role!

Microscopy skills and knowledge are used in a wide variety of jobs and careers, from developing microscopes and using them for research, to selling or repairing them.

Now you can share details of your role with fellow microscopists using the RMS website, and help inspire others to pursue careers in microscopy, imaging and flow cytometry.

All you have to do is visit our profiles page and fill in the simple form - including a profile photo.

Submit your profile

RMS staff team welcomes Kitty Ng! A very warm welcome to Kitty Ng, who has joined the RMS team as Event Exhibition Assistant.

Kitty will be helping deliver the many exhibitions associated with the RMS’s busy events schedule, working closely with colleagues in the RMS Events team and with our sponsor companies.

Kitty recently moved to the UK from Hong Kong, where she worked for 15 years for an events agency, staging conferences and

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ISSUE 76 DECEMBER 2024

exhibitions on behalf of IT companies.

She said: “I’ve really enjoyed my first few weeks here, getting to know my new colleagues in the RMS team as well as our commercial partners.

“This is a new area for me and I’m really looking forward to learning more about the microscopy community and contributing to the important work of the RMS.” Kitty Ng.

RMS partners with global database for jobs, events, tools and training MicroscopyDB resources now accessible on RMS website A

global

database

for

jobs,

vacancies, tools and education resources with a global community, providing a one-stop shop for events,

tools and training is now available on the RMS website, making it easier than ever before to access microscopy resources and information.

all levels of microscopy user.

RMS website users will still be able keep track of all the Society’s upcoming meetings, conferences and courses by visiting our Events Calendar.

The Society’s partnership with Microscopy DB, a community-driven repository of online microscopy resources, will also unlock a wider range of materials and information from around the world.

The database enables users to share events, job

RMS training survey attracts more than 500 responses!

Prize-draw winner receives £100 gift voucher!

The

RMS

has

successfully

completed

Development - Focused Interest Groups (PTDFIG), I’d like to say how grateful we are for the a

comprehensive survey aimed at identifying current demands and gaps in microscopy training.

overwhelming response.”

She added: “The Society aims to use these findings to tailor its training programmes, ensuring they

With more than 500 responses, the survey provides

meet the evolving needs of microscopists across

valuable insights into the practical preferences of

various sectors.”

professionals in the field.

The results of the survey will be published on the

The

15-minute

survey, designed

to

inform

future RMS course offerings, garnered significant participation from the microscopy community with responses from all corners of the globe – 46

RMS website in due course.

For more information, contact georgina@rms.org.uk

countries to be exact!

As an incentive, participants were offered the chance to win a £100 Amazon voucher in a random prize-draw, and we’re pleased to announce the lucky winner was Pier Andrée Penttilä from the LMB in Cambridge.

Georgina Fletcher, the RMS contact for the survey, said: “On behalf of the Professional Training and

75

NEWS

RMS Council Member Paul Verkade elected to European Microscopy Society (EMS) Executive Board The RMS is very pleased to learn that Professor

bringing together a number of different microscopy

Paul Verkade has joined the Executive Board of the

societies – including the RMS - and helping to build

European Microscopy Society (EMS).

a dynamic community covering all branches of

Paul, who is a long-standing member of the RMS

microscopy and across the sciences.”

Electron Microscopy Committee and a current

Paul is a Professor of Bioimaging at the University

member of the RMS Council, was elected to his

of Bristol, UK. He has been working in the field of

new post during the EMS General Assembly at

microscopy from the start of his scientific career

emc2024 in Copenhagen.

and over the last 15 years has established himself as

The EMS Executive Board is comprised of members representing a number of different countries across

one of the leaders in the field of Correlative Light Electron Microscopy (CLEM).

Europe, drawn from different areas of microscopy within Material, Life Sciences and Instrumentation areas.

Paul said: “It’s a real honour to be asked to join the board, and I look forward to working with my new colleagues in support of microscopy across the whole of Europe. The EMS is a key organisation -

European Microscopy Society (EMS) launches 2024 Outstanding Paper Award Prize will be awarded to papers containing original work in the field of microscopy

The Executive Board of the European Microscopy

• Materials Sciences • Life Sciences

Society (EMS) is very pleased to announce

The prize consists of €1,000 plus a glass award

the “Outstanding Paper Award” (OPA) for papers

plaque for the first author(s) (per awarded paper)

published in 2024.

for each category and certificates for all authors.

The prize will be awarded to papers containing original work in the field of microscopy which will be judged on scientific merit, technical and general quality, expected impact, originality and relevance to microscopy. One paper will be chosen from each of the following categories:

76

• Instrumentation and Technique Development

ISSUE 76 DECEMBER 2024

These glass award plaques will be presented during the next EMS extension: 17th Multinational Congress on Microscopy to be held in Portorož, Slovenia on 7 – 12 September, 2025.

Find out more about the rules and how to enter.

R E P O RT

RMS Technical Specialist Job Shadowing Program Report: Advanced Imaging Resource, Institute of Genetics and Cancer

By Daniel Thédié, post-doc at the University of Edinburgh

M

y one-week visit to IGC is coming to an end, and it has been a great week filled with new experiences and interesting discussions!

I am a post-doc at the University of Edinburgh's

shoes by benchmarking a new software for single-

school of biological sciences, working on DNA

molecule localisation on two of the facility's image

repair and bacteria. I use a lot of microscopy and

analysis computers. This was great hands-on

image analysis, and I have been wanting to transition

experience of installing and testing software with

towards a facility position - assisting users with

potential users in mind, and gave me an opportunity

their image analysis questions, testing new tools,

to discuss ways of improving the computing power

implementing new workflows. I therefore applied

of the facility's virtual machine with Brian Wallace

with Ann Wheeler's help to the Royal Microscopical

from Information Services.

Society's technical job shadowing scheme, and got to spend a week at the Advanced Imaging Resource at IGC. I had a great time shadowing the bioimage analyst Laura Murphy, and meeting with IGC staff working in and around image analysis.

meeting with other IGC staff, discussing their professional experiences and their everyday work.

Highlights of this were a particularly informative discussion with Murray Wham on designing web

I really enjoyed sitting with Laura and looking at

applications for researchers, and chats with Fiona

different images and queries she received from

Inglis, Leo Leplat and Alan O'Callaghan on the

users. I find the variety in the projects she's working

development of QuPath.These discussions made me

with really motivating, from histopathology whole-

want to learn more about software development,

slide imaging to nuclear protein organisation, to

and left me with multiple new concepts and avenues

single-molecule super-resolution, and more. During

to explore in the future.

the week we held a drop-in clinic session, where researchers could bring their microscopy images, and I enjoyed working out with them what was the best approach to answer their biological questions with the data they collected.

I also had the chance to get into an image analyst’s

78

A major part of the shadowing experience was

ISSUE 76 DECEMBER 2024

All through my visit, I got to see what a vibrant and friendly place IGC is. Researchers interacted easily in formal meetings as well as informal encounters, creating a pleasant and stimulating environment.

This was particularly clear at the pizza party organised by the IGC social committee, which was

really cheerful. The atmosphere made me feel very

gave me some of their time, let me peek over their

welcome during the whole week, which allowed me

shoulder at what they were doing, and explained

to make the most of my visit.

the joys and challenges of their everyday work.

I would like to heartily thank Ann Wheeler and Laura

And finally, thank you to the Royal Microscopical Society for allowing me to have this job shadowing

Murphy for welcoming me this week, taking the time

opportunity through their funded program. It has

to show me around, and organising meetings so I

been a truly enriching experience, and I would

could get the best experience possible in this short

recommend it to anyone who is curious to learn

time. I would also like to thank all the people who

more about different careers or workplaces.

Daniel spent a week at the Advanced Imaging Resource at IGC, shadowing bioimage analyst Laura Murphy, with whom he is pictured here.

79

Hocus Pocus

By Lola Molina Fernández, Centro de Instrumentación Científica, University of Granada

Image shortlisted in the 2023 RMS Scientific Imaging Competition (Electron Microscopy, Life Sciences category). This is an SEM image showcasing the morphology of Freesia x hybrid stigma cells, from which flowers grow. The magical aspect of this image is the substances in the stigma's glandular tissue, which detect compatible pollen. The cell texture's brightness indicates the distribution of elements like calcium, phosphorus, and sodium.

Coauthor: Isabel Sánchez Almazo.

Quanta 650 FEG (Thermofisher Scientific-FEI) This picture is the result of the overlay of secundary and backscatter electron images.

Creating an EM facility: A dual perspective Erin M Tranfield, VIB BioImaging Core, Ghent, Belgium (formerly Electron Microscopy Facility, Instituto Gulbenkian de Ciência, Oeiras, Portugal) Jon Moss, 3D Volume Electron Microscopy Capability (Proteomics and Metabolomics Facility), Roslin Institute, University of Edinburgh, Scotland

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Erin Tranfiel.

Jon Moss.

How does an Electron Microscopy (EM) facility come into being? For many established facilities it feels as though they have always existed, sewn into the fabric of institutes, departments and universities.

But scratch beneath the surface and there are a myriad of stories, of struggles and successes, of shrewdness and invention that go into making a facility work well. In this article we hope to share

our diverse experiences founding an EM facility with the hope of helping others on a similar journey. Jon is in the midst of the process and Erin is 11 years down the line but still learning as she goes.

ISSUE 76 DECEMBER 2024

Managing an electron microscopy facility is as varied and interesting as it is complicated and challenging.

Bringing a facility from vision to reality presents its

own unique set of challenges, particularly when you don’t know where to turn for advice. Our hope is that through this article we can demystify the process of founding and running a (successful) electron microscopy facility by sharing our own experiences and reflections on what has gone well and badly for us, with an overarching goal of making things easier for those who are tasked with doing the same thing in the future.

Before we start, we should introduce ourselves.

We first met at the 2023 Microscience Microscopy Congress (mmc) in Manchester. The RMS excels at getting people together and our collaboration is a great example of that. Jon was interested in joining the TechEM Seminar series that Erin had discussed in her talk at the congress, and he mentioned to her that he was one year into setting up EM capabilities at The Roslin Institute at The University of Edinburgh. Little did he know that he was in the midst of a kindred spirit, as Erin had done the same thing 10 years previously, at the Instituto Gulbenkian de Ciência in Lisbon.

Jon and Erin both trained in EM during their PhDs; Erin at the University of British Columbia under Dr. David Walker and Jon at the University of Oxford under Prof. Paul Bolam. After each completing two post-doctoral fellowships, they were invited to set up their respective EM facilities, and this is where the story will begin. In the sections that

follow Jon and Erin will compare and contrast their experiences setting up their electron microscopy facilities. They hope this dual narrative is helpful, or at least entertaining. The sections below will be written in a first-person narrative, with the person speaking identified at the start of the section.

Facility inception through to readiness

Jon: My first involvement with the new EM capabilities was in the summer of 2021, helping with the procurement of the electron microscope and associated equipment. The technical needs were dictated by three key questions: Q1: Which workflows did we want to provide? Q2: What portfolio would be of most use to the local and wider scientific community? Q3: Could we fill a technical niche that existed in the local area? We focussed on two main workflows: serial blockface scanning EM (SBF-SEM) and correlative array tomography (CAT), as neither of these workflows were available in the local vicinity and both would augment many existing research projects. We identified comparable technologies from different companies, and evaluated them against each other to find the best option. As a result, an order was placed in December 2021 for the scanning electron microscope (with SBF and transmission EM imaging capabilities), light microscope (for correlative work), ultramicrotome (for tissue preparation), computer

Building a facility brick by brick: Although the critical path for a facility is that of project management, from research question through to visible outputs, there are many (often unseen) facility activities that aid its smooth progression. These evolve over time with the demands of projects and the personnel and equipment available. Each activity can be broken down further; for instance, ‘Health & safety’ includes writing and updating risk assessments, training staff in good practice, logging reagent usage and expiry, inspections and audits. Additionally, ‘Networks and outreach’ includes conferences and specialised seminar series such as the TechEM Seminar Series, and ‘Problem solving’ includes optimisation of protocols.The result of every process invariably feeds back to itself and other processes to improve and refine overall performance.

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hardware and software (including an analysis workstation), consumables (such as diamond knives), and a 4-year service package.

Getting this equipment, however, is only a fraction of the story when it comes to readiness to provide a service, and 2022 saw the equipment arrive in the Spring, me arrive in the Summer, and basic training to be completed by the Autumn. We then sourced additional equipment (vibratome, sputter coater, and critical point dryer) to bring all processing in-house and remove hour-long trips to other campuses. Before these arrived in Spring 2023, we got other important things in place. We defined a fair costing structure, ordered consumables, tested protocols (provided by others in the volume EM community), wrote risk assessments, and met with multiple researchers to start projects. All this meant that, when the final machines were installed, we had samples ready for them and could immediately begin producing project outputs.

If I were to do it again, I would be more rigorous in identifying earlier which extra pieces of equipment would help to improve the efficiency of the workflows. I would also ask for more advice from those who had done the same before. There are so many small details to consider when starting from scratch that it is easy to miss something of real importance along the way.

Facility organisation

Erin: In 2013 when we started the IGC EM Facility, we invested a lot of time planning how we would track experiments, communicate project progress and archive completed experiments. We started a sequential sample numbering system and a database that detailed the requesting scientist, the sample details, the sample preparation protocol used, the experimental date, the facility technical expert responsible and the experiment number for every single sample that came to the facility. In parallel to this we have an inventory of all our reagents and a history of the lot numbers of those reagents.

This system has served us very well over the last 11 years and we have made only a few changes in response to evolving needs of our community and constructive feedback.

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Consequently, we can provide our investigators with everything they could ever want to know about the work. This level of tracking is not hard to set up and once it is in place, it takes only a little effort to maintain but it builds a very complete documentation system within the facility. If we wanted to reconstruct this in hindsight it would be almost impossible to do. Spending the time to define how we wanted to work and implementing a robust system that is always open to improvements was one of the best things we did at the start of our facility. If I could go back in time and change just one thing, I would have a tracking system for the model organism, and the technique(s) used. This would allow me today to easily find a previous project that is similar to one we are about to start so I can compare protocols and avoid reinventing the wheel.

Growth of networks

Jon: Keeping track of protocols for use with future projects is a tip I shall be taking from Erin. It is definitely not a case of one-protocol-fits-all. Landing on the right protocol for a specific sample wasn’t straight-forward for either of us at the beginning of our facility management journeys. We have both relied on our collaborative contacts to guide us along the right track.

It was at the RMS BioImagingUK meeting in September 2022 that I first met many like-minded people from other microscopy facilities. They were more than happy to give advice and put me in touch with the right people or protocols. Being aware of who is best to ask about a certain technique or technology is a valuable skill and before long you will become the one with knowledge to share.

These community bonds are strengthened with every connection made (and every piece of advice given or received), and properly-cultivated, they flourish into a better understanding of how best to perform our roles.

These chances for face-to-face interactions run hand-in-hand with several online initiatives. Indeed, my fellow co-author, Erin, pioneered the TechEM online seminar series to keep conversations about EM techniques, technologies, and training going in the times of the COVID-19 pandemic. So valuable

Useful networks for starting a Bio-EM facility: These are a few of the key networks we have learnt from and give back to, that have helped us along the way, giving support and guidance on anything from sample preparation to publicising achievements.

were these discussions, the TechEM Seminars have persisted longer than any lockdown, and now offer many stimulating presentations on a variety of EMrelated subjects. Many other groups and resources support the imaging community and the table above lists some of those we have been (or intend to be) involved with.

Erin and I both agree that microscopy facilities should not operate in isolation. It is through a strong network of colleagues that experiences can be shared, and challenging projects overcome.

Defining the facility

Jon: Meeting people through these networks has shown me how diverse the specialties of EM facilities can be. The question then becomes: Where do I fit into all of this? I can’t do everything. Do I need a ‘special skill’ to best serve researchers or is it better to do the simple things well?

As is the answer to many things, the conclusion I came to was ‘a bit of both’. By showing I can do the relatively simple things well I earn the trust of the community, and that then gives me the freedom to express some individuality in defining the focus of our operations. One benefit of setting up EM capabilities in the same university I’d been working at for the last five years was that my contacts with certain networks, particularly the Edinburgh Neuroscience community, were already well established. Many projects have now resulted from these long-term relationships built on mutual appreciation. Equally, I am based at the Roslin

Institute campus of the University, famed for its work on Dolly the sheep, and can thus be deeply involved in both veterinary science and the use of animal models to better inform on human health.

Therefore, I need look no further than the projects landing in my inbox, for the special skills I can work on developing. To date, I have had enquiries about tissue or cells from nematodes, zebrafish, mice, rats, chickens, sheep, pigs, horses, dolphins and humans.

Every sample I work with has its own intricacies and I thoroughly enjoy trying to get the most out of the sample for the collaborating researchers. But project-type is only one way of defining a facility.

I will still need to decide on the balance between academic and commercial projects and which techniques benefit the greatest number of scientists.

What I have already experienced is that, through equipment and training, I can pivot to adapt to the demands of new projects.

Erin: I fully agree with what Jon has written above and I would like to add an important emphasis that I strongly believe a facility must be defined by the needs of the community it serves. The perfect facility not only serves the needs of the vast majority of its users, it also has the talent of incorporating new technologies that will enhance the scientific capabilities of the research community.

Marketing the facility

Erin: I believe the two essential things needed for marketing a facility are excellent work quality and an informative, easy to find website.

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Since the IGC facility started in 2013, we have always aimed to help scientists address their biological questions on the shortest timeline, tightest budget with the highest quality work possible.

In our experience, word spread quickly that the facility provided high-quality, full-service support in electron microscopy for anyone in the research community. As groups shared their experiences by word of mouth or scientific presentations, more people asked the facility team for technical support. I was invited to teach in many Masters and PhD Programs in the Lisbon area which further broadened the awareness of the range of techniques and the nature of the technical support we provide to the local scientific community. Overall, I feel the excellence of our work was a very effective selfperpetuating marketing tool.

The second point - our website - was essential in describing the range of projects we can do and I frequently received email inquiries from the website in the first 6 years. Recently the institute changed the website to a less informative, more corporate website and I noticed the number of inquiries for the facility decreased. I connect these two things.

The decreased website contact did not cause a worrying drop in facility usage because after 11 years the facility is well known in the community but it is clear to me that we had a lot more interest in the past when we had a more informative and detailed website the community could access. Making information accessible, simple and understandable was very useful in attracting people to the facility and attracting projects.

Jon: Erin makes a good point about the quality of work being a good marketing tool. Many enquiries I receive about new projects come via word-of-mouth recommendations from previous collaborators.

Responsibilities

Erin:At times it feels that facility users expect facility staff to be responsible for sample preparation, experiment coordination and project management.

Facility staff should also help with data storage, data analysis, standardisation of protocols, training, teaching, as well as chemical and radiation safety.

The facility head should be responsible for all

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that as well as scientific dissemination, protecting the health and well-being of the facility staff, maintenance of equipment, growth of the facility, fairness to all people wanting to access the facility as well as defining and implementing low-cost access that allows full cost accountability to the leaders of institutes. Unfortunately, when working in a small facility of 2-3 people, this wish list of roles is almost impossible. My way of trying to balance the wished-for support with what we can realistically do is to support the work that keeps the scientists answering their questions, and keeps the equipment being used. Yes, we could invest our time analysing data but then who is supporting the work at the microscopes? If we are modelling results, then who is training users or doing sample processing? Yes, we could teach in every course we are invited to but an empty facility with no support staff helps no one. Therefore, I tried to strategically pick where we invest our time aiming to support our facility vision, fulfilling the mandate we received from our leadership and keeping our key performance indicators (number of usage hours, number of projects, number of output papers) as high as possible. This usually means I am unpopular with some of our facility users, but that is a situation I have learned to accept.

Chance for innovation and development

Erin: Core facilities exist to provide service to the scientific community so I believe providing excellent service should be the main work that is done by the core facility team. Yet to provide excellent service we also need to be aware of new techniques that are being developed, we need to optimise procedures and ensure technical team members are trained to do techniques with accuracy and efficiency. Protocol optimisation and team training take time away from standard services, yet I think they are time well invested when the result is we are growing the breadth of techniques we can provide, and planning for the overall operation and longevity of the facility.

These projects can also be very important for the skill development and motivation of each team member. For a 2-3 staff facility like ours, we aim for 70% routine work, 20% technique optimization /

reagent testing and 10% innovation.

When technical facility teams are in the range of 10-12 people, there may be time to invest in technique innovation and development but this needs to be in line with the overall mandate of that specific core facility and the broader vision of the institute's direction. One last thing I would like to emphasise is that development efforts require a

substantial time commitment to give the work a chance of being successful and leading to technical steps forward. There is no point in investing a small effort in development projects because the lack of outcomes will most probably bring the value of that investment into question. Invest fully or not at all.

Lessons we have learned Erin 1. Take on one new challenge at a time. I advise that you do not try to implement 10 news things at the same time. Instead, pick one, implement it well, then move on to the next item on your list.

2. Quiet users = happy users. People do not often give compliments or show appreciation for your work.

However, if no one is complaining then people are happy.

3. Document everything very well. Regardless of intent, experience suggests you will not remember what you did six months ago.

My overall advice if you are setting up a new facility is to know your user community, know their scientific needs, the available budgets for facility usage and then trust your instincts. I presume you are an expert in your technology with a lot of experience using it. Let that experience guide you. Build the facility that would best support the research community around you.

On top of that, find someone who works differently from you, and make sure your facility model works for them too.

Jon 1. At first, lessons come thick and fast. I am not the same person I was three months ago and I’m sure I will be different again three months from now. Be willing to adapt and learn amid the shifting sands.

2. Build a strong network of technical experts.You do not need to know all the answers, but it helps to know who has the answers.

3. Don’t expect perfection from Day One. It is tempting to measure yourself against those you admire.

It’s only after talking with them that you appreciate how long and winding their journeys were.

Overall, I would say keeping an open mind to new opportunities and being adaptable when solving problems (methodological and logistical) would hold you in good stead. If you can grow hand in hand with the facility then that can benefit you both.

Also, being proactive in every activity will serve you well. Facilities that just tread water will fade to obsolescence. Engaging with networks and volunteering to take on extra tasks will benefit you greatly, sometimes in ways you won’t first envisage.

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R E P O RT

High School student steals the show at M&M 2024 Poster session

A

16-year-old student made a special appearance as the youngest poster presenter at Microscopy & Microanalysis (M&M) 2024 – the premier microscopy event in the United States.

(DSTRI), working alongside the paper’s co-author,

Jonas Cruz was the star turn during the final

micrographs, referencing the presence of osteocytes,

poster session of the congress, engaging with

nerve filaments, vessels and collagen-filled shards

fellow attendees and discussing his paper, titled

following the latest analyses of bone fragments.

‘Astonishing soft tissue permanence in surface-

Jonas, of El Paso,Texas, said: “I have had an interest in

collected Triceratops horn shards from Hell Creek,

dinosaurs, probably since I was five years old. When

Montana’.

I was around eight or nine, my mom took me to

His appearance at M&M 2024, in Cleveland, Ohio, followed two spells of fieldwork as an intern with the Dinosaur Soft Tissue Research Institute

Jonas attended M&M 2024 with his mum, Jennifer, and sister, Aria.

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Mark Armitage. Excavations at the Hell Creek site have famously yielded examples of soft tissue elements from a number of bone samples, sparking widespread interest and scientific debate.

Jonas’s poster featured a series of eye-catching

my first dinosaur symposium at the university, and that captured my interest.

“So I have always been interested in dinosaurs but

Jonas holding a triceratops bone fragment.

there was never really a proper connection until I

interact with palaeontology from a more biological

went on the dig, which was a dream to me.”

perspective. Microscopy is a well-rounded field of

Commenting on the findings reported in his poster, Jonas said: “I think it shows dinosaurs in a different

science, and also opens up other areas of interest like forensics and genetics.”

light in terms of the fact that these aren’t rocks – they are still bone, so there is more of an immediate connection.

“It’s very inspiring to think that maybe one day it might be possible to find DNA or chromosomes, or for instance, what this might tell us about the past in terms of how the bone structure compares to modern birds.”

Still a high school student, Jonas plans to study biology for his undergraduate degree, and is particularly interested in genetics and exploring forensic science. One potential area of research he would like to become involved in is the prevention of genetic disorders before birth.

Jonas presenting his poster at M&M 2024.

Reflecting on his appearance at M&M 2024 Jonas added: “It was extremely inspiring and I saw for myself how many career opportunities there are

He said: “I originally wanted to be a palaeontologist;

in microscopy and how it is so multi-disciplinary.

however, I found that I didn’t like the geology aspect

Everything

of it at all, although I loved everything else about

particularly the level of diversity, and the amount

the fieldwork. Adding and learning microscopy

of collaboration on display. It certainly opened my

has given me more options in terms of how I can

eyes in terms of career choices and opportunities.”

was

memorable

about

M&M

–

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‘The Microscopists’ podcast tackles mental health in special episode Candid interviews with leading researchers shine light on important subject

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A

popular podcast presented by RMS President Peter O’Toole has turned its attentions to the pressing issue of mental health within the research community.

In the special episode of ‘The Microscopists’

we have championed researchers’ well-being and

(produced by Bitesize Bio, the University of York,

mental health for over 15 years and set out to raise

and sponsored by Zeiss), Pete interviews two

awareness of the harms that can result from the

internationally renowned researchers, Dr Beth

pressures of the research environment.”

Cimini (Senior Group Leader at the Broad Institute of MIT and Harvard) and Dr Kedar Narayan (Group Leader at the Center for Molecular Microscopy),

Daniel

Hartmann,

Marketing

Specialist

for

Microscopy in the Life Sciences at ZEISS, added:

who shares his experience with debilitating anxiety.

“The Microscopists podcast always inspires candid, fun, and engaging conversations. While this episode tackles a more serious topic, I hope it will encourage listeners to seek help if they are struggling.”

The three researchers speak candidly about

In addition to shedding light on the challenges of

their mental health struggles and the impact on

scientific research and seeking to reduce the stigma

their work. By encouraging an open dialogue, the

associated with mental illnesses, the podcast also

episode aims to inspire cultural change and practical

reflects a broader commitment by Bitesize Bio, the

support for mental health in scientific research

University of York, and ZEISS to champion research

environments.The discussion also highlights the fact

environments

that mental health problems can affect scientists at

professionally and personally. As mental health

all stages of their careers.

continues to be a global concern, initiatives like

about their experiences with depression.

They are later joined by Jason Rodgers (Podcast Producer

at

Bitesize

Bio

and

Postgraduate

Researcher at Liverpool John Moores University),

Pete said: “I thought this was a really important topic to cover, and credit should go to Beth, Kedar,

where

researchers

can

thrive

these highlight the importance of support systems and open communication in mental health recovery.

and Jason for being brave and open to discussing

The Microscopists Mental Health Special with

their history, especially as, for some, this was the

Beth Cimini, Kedar Narayan, and Jason Rodgers is

first time that they had spoken about it,”

available now on the Bitesize Bio website and all

He added: “Despite being a very serious issue, the guests kept things entertaining and, at times, lighthearted. It shows that mental health issues do not need to get in the way of being highly successful scientists. It was great to hear how they, or those around them, realised that they needed to seek support.”

popular podcast platforms.

About Bitesize Bio: Bitesize Bio is an online community dedicated to providing bioscientists with high-quality resources and educational content. With a mission to encourage knowledge sharing and collaboration in science, it offers a wealth of practical advice, tips,

Dr Nick Oswald, Founder and Director of Bitesize

and insights that are easily accessible and applicable

Bio said: “The pressures of working in research are

to everyday lab work. The company’s vision is to

well-known, but the mental health consequences

become the premier global platform for mentoring,

are not widely spoken about. That’s why, at Bitesize

practical knowledge sharing, and accessibility in

Bio, we don’t just focus on improving technical skills;

bioscience. Find out more at: www.bitesizebio.com

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C O M PA N Y N E W S

Telight welcomes Antony Edwards!

Telight is pleased to introduce their new colleague responsible for developing sales in the UK market.

Antony Edwards is a Fellow of the Royal Microscopy Society. With extensive expertise in advanced biological and electron microscopy, he brings valuable experience in sales management, business development and the sale of highly specialised scientific equipment. Antony Edwards sold the first commercial two-photon microscope to the University of Bristol back in 1996 when he worked for Bio-Rad Laboratory in the UK. At Thermo Noran UK, he increased sales and secured the first sale of the OZ confocal microscope with a video stage outside the US. Later, at Image Solutions UK Ltd, he managed the successful integration of DeltaVision into GE Healthcare, leading to its significant economic growth in Western Europe. www.telight.eu

Biologists @ 100 conference, 24-27 March 2025, ACC Liverpool, UK (BSCB) and the British Society for Developmental Biology (BSDB). It will further include a Society for Experimental Biology (SEB) one-day Satellite Meeting ‘Experimental biology and impact: solutions to climate change and biodiversity loss’, the Journal of Experimental Biology (JEB) Symposium ‘Sensory perception in a changing world’, and a one-day Disease Models & Mechanisms (DMM) programme ‘Interdisciplinary

approaches

to

combatting

antimicrobial resistance’.

2025 will mark the 100-year anniversary of The Company of Biologists. As part of our celebrations, the Company will be organising Biologists @ 100, a unique conference that will bring together our different communities.

The conference will incorporate the Spring Meetings of the British Society for Cell Biology

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In the plenary sessions, the keynote speakers will consider topics of importance to the whole biological community: climate change and biodiversity, health and disease and emerging technologies.

Registration and abstract submission are now open.

To view the programme and register your interest, visit https://biologists.com/100-years/conference.

Nikon Europe B.V. (Nikon) is pleased to announce the opening of three Nikon BioImaging Lab (NBIL) sites in Europe The NBIL is a Contract Research Organisation (CRO) that provides microscope-based imaging and analysis services to the biotech, pharma, and larger research communities, offering contract research services from the company that knows imaging.The new NBIL sites, located at BioLabs Heidelberg in Germany, iCITY Basel in Switzerland, and Babraham Research Campus in Cambridge UK, are an expansion of the NBIL Europe main hub located at Leiden BioScience Park in the Netherlands.

at Nikon Europe B.V. NBILs provide contract research services for assay development as well as microscope-based imaging and analysis to the biotech, pharma, and larger research communities. The opening of these three new labs expands the full-service capabilities Nikon can offer to scientists and researchers, which now includes access to cutting-edge microscopy instrumentation and services of expert biologists and microscopists, who are available to provide

BioLabs Heidelberg, iCITY Basel and Babraham

quality cell culture, sample preparation, data

Research Campus are three hubs for outstanding

acquisition, and data analysis services.

science. All establishments have been designed with life science researchers in mind and offer flexible spaces for biotech companies, big and small, making them perfect locations to partner with Nikon on this expansion.

The NBILs at BioLabs Heidelberg and iCITY Basel are now open. NBIL at BioLabs Heidelberg will hold an engaging introductory workshop on 11th September with guest speakers and hands-on sessions with the ECLIPSE Ji Digital Microscope.

“‘Nikon are very excited to expand the level of

Registration for the event at BioLabs is open now

research support we can offer to the scientific

here. The lab at Babraham Research Campus is due

community through opening three new NBILs at

to open on 23rd September with an exciting opening

these prestigious facilities. We hope it strengthens

event, including talks from leading researchers and

our collaboration with BioLabs, iCITY and Babraham,

panel discussions.

and enhances the research capabilities offered to the

https://www.microscope.healthcare.

drug discovery and biotech companies throughout Europe.” said Daniel Ciepielewski, General Manager

nikon.com/en_EU/

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C O M PA N Y N E W S

QPI in BioImaging series Jaromír Gumelec, an advanced user of our microscope from Masaryk University, got the opportunity to present his research as a webinar for the EuroBioimaging scientific infrastructure, of which we are part of the industrial council. His research focuses on the mechanical properties of cells and their influence on cancer progression. He uses the Q-Phase instrument to monitor shear stress in cells and their deformation. The advantage of this method is that it allows the analysis of large numbers of cells. Watch the full webinar in the following link.

www.telight.eu

FocalPlane – a site for the microscopy community FocalPlane is an online community site for anyone who uses microscopy in their research. Since its launch in 2020, the site has become a platform for bringing together the microscopy community.

Our blog posts are a key feature of FocalPlane.These posts fall into several categories including ‘News’, ‘Tools’, ‘How to’ and ‘Interviews’. Anyone from the community can post, allowing them to showcase their research and tools in an informal way, and to a broad audience. The in-house team also highlights the latest research in a fortnightly preprint list, as well as hosting a regular series that showcases core facilities and their staff. Our team of FocalPlane correspondents have also contributed a range of posts, including interviews that highlight scientists from across the global microscopy community.

FocalPlane also runs a regular webinar series. We recently hosted talks on outreach, education, open microscopy, data management and reproducibility, as well as a webinar celebrating the Journal of Cell Science Special Issue: Imaging Cell Architecture and Dynamics. You can view the recordings of our webinars on FocalPlane or on The Company of Biologists’ YouTube channel. We are in the process of planning our 2025 schedule, so please let us

know if you have any requests for the series.

The FocalPlane Network, an international directory of researchers with microscopy expertise including developers, imaging scientists, bioimage analysts and biologists, is another important feature of our community site. We encourage you to join and use the Network to facilitate promotion and networking within the community and to search for conference speakers, committee members, reviewers or collaborators.

More recently, we added jobs and events boards to FocalPlane. We now host microscopy boards as part of the MicroscopyDB partnership, and cell biology-specific versions with our host, Journal of Cell Science. You can also search for community resources, educational resources and tools in our MicroList resource database, thanks to our recent merger with MicroList.

Finally, please remember that FocalPlane is your site.

Once registered, you can freely publish blog posts, resource cards and cell biology jobs and events. If you have any comments, suggestions or requests, please get in touch at focalplane@biologists.com. https://focalplane.biologists.com/

If you would like your Company News to appear on these pages, please contact infocus Magazine at advertising@infocus.org.uk The announcements in this Section are compiled by the manufacturers. They in no way represent a recommendation by the Royal Microscopical Society for any particular instrument or equipment. The Royal Microscopical Society does not endorse, support, recommend or verify the information provided on these pages.

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Mini2P Miniature Two-Photon Microscope Designed for Calcium Imaging in Freely Moving Specimens

Mini2P Miniature Two-Photon Microscope

Thorlabs’ Miniature Two-Photon Imaging System (Mini2P) is a fast, high-resolution miniscope designed for in vivo two-photon imaging of freely moving specimens. The lightweight, head-mounted design allows for stable calcium imaging without impediment to the sample. The Mini2P enables hundreds of neurons to be monitored in a single field of view, while visualization of up to a thousand cells is achievable with multiplane imaging controlled through the built-in microtunable lens.

Product Features Compact Design Featuring On-Board Electronics for Scanning and Signal Detection

Simultaneous Measurement of Hundreds of Neurons is Possible High-Sensitivity Detection with an On-Board, Dual-Color SiPM Fast Multiplane Imaging with a Microtunable Focusing Lens Two MEMS Laser Scanning Options: 40 Hz Fast Scanning or Large 0.25 mm2 Field of View

Spontaneous Neuronal Activity in the Somatosensory Cortex of a Mouse Expressing GCamp6 Imaged with the Mini2P

Multiple Interchangeable Objectives

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Benefit from a 6.5x zoom and user-friendly Metlogix

Available for just £900 with a choice of stands and

software.

lenses.

visioneng.com

➔ EVO Cam Series: expanded digital microscope options:

96

Choose the perfect EVO Cam system to meet your

ISSUE 76 DECEMBER 2024

LightSpeed Mode for UltraMicroscope Blaze™: Faster than ever, precise as always Experience unprecedented 3D imaging speeds

synchronisation eliminates the need for the stage

with the LightSpeed Mode, a groundbreaking

to stop and restart, significantly reducing the time

advancement in the UltraMicroscope technology.

required to capture a 3D image stack, even for large

Powered by over a decade of innovation and

samples. The image quality and resolution remain

customer feedback, this game-changing feature

unaffected throughout this process.

delivers the fastest acquisition rate ever seen with the UltraMicroscope. This innovation achieves unparalleled speed through a synchronised stage and camera, without compromising image quality or resolution.

All datasets generated in LightSpeed Mode can be stitched and processed using our new software, MACS iQ View - 3D Large Volume. The software provides dedicated post-processing workflows and batch processing capabilities, enabling users

The LightSpeed Mode can speed up image

to queue and initiate various workflows across

acquisition by up to 60 times compared to the

multiple datasets. This feature proves invaluable

classic high-resolution mode (Dynamic Focus),

when dealing with large volumes of data and imaging

making the UltraMicroscope Blaze the fastest light

multiple samples, ensuring a smooth and efficient

sheet microscope on the market.

processing workflow.

This impressive speed is achieved by continuously

For more information visit here.

moving the UltraMicroscope stage while the

www.miltenyibiotec.com

camera

captures

images

simultaneously. This

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NEW PRODUCTS

New Performance-Enhanced Marana BSI sCMOS Camera Oxford Instruments Andor, a world leader in scientific imaging solutions, has announced the launch of a performance-enhanced back-illuminated sCMOS camera, further strengthening its broad portfolio of cameras for Physical Sciences and Astronomy.

concentrations of species.

A new High-Speed mode has been implemented to meet the needs of fast imaging applications such as trapped ion/atom quantum computing, solar astronomy, fast spectroscopy or hyperspectral imaging. By combining this mode with a 2-lane

Marana 4.2B-6 Back-illuminated sCMOS: Now Even

CoaXPress connection, 135 fps of sustained and

Faster, More Sensitive and with Long Exposure

stable high-speed operation is now possible.

Capability

Furthermore, a new Long Exposure Mode has

The performance of the Marana 4.2B-6 back-

been implemented which markedly enhances the

illuminated 4.2 Megapixel sCMOS model has been

exposure flexibility of Marana 4.2B-6. Amplifier

significantly enhanced to widen its application

glow has been a problem that has plagued most

appeal within Physical Sciences and Astronomy. A

sCMOS sensors on the market.This new mode goes

new Low Noise Mode reduces the read noise to

a long way to suppressing the effect of amplifier

1.0e-. When combined with market-leading -45°C

glow under longer exposure conditions. This is

vacuum cooling and 95% QE, this pushes the limits of

particularly relevant for fields such as astronomy

detection further, even under the most challenging,

and low light luminescence detection.

light starved imaging applications, enabling tracking of smaller Space Debris or NEOs, shorter exposures, lower illumination powers to protect photosensitive samples or the detection of trace

A ‘Global Clear’ mode has now been implemented for the Rolling Shutter sensor type. This mode purges charge from all rows of the sensor simultaneously at the exposure start. It can be used alongside

a

pulsed/triggerable

light source, such as LED or Laser, to simulate a Global Shutter mechanism, useful for achieving tight synchronisation

with

other equipment and minimising

exposure

‘dead times’. https://andor. oxinst.com/

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ISSUE 76 DECEMBER 2024

Wiley and Digital Surf release new end-to-end software solution that unifies microscopy and spectral analysis workflows Wiley, one of the world’s largest publishers and a

to go from microscopic and hyperspectral images

global leader in research and learning, and Digital

to spectral analysis across multiple microscopies

Surf, editor of analysis software solutions for

and spectroscopies in a unified workflow creates

microscopy and spectroscopy, have announced

tremendous efficiencies for your lab. Wiley

the release of Wiley Surface-to-Spectral Analysis,

Surface-to-Spectral

a complete correlation & spectroscopy analysis

Wiley’s KnowItAll spectral analysis software and

software solution for microscopy.

comprehensive, quality databases, equips labs with

Wiley Surface-to-Spectral Analysis provides a comprehensive, powerful solution to process,

Analysis,

combined

with

an unmatched end-to-end solution from surface to spectral analysis.”

combine, and analyse images and data from various

Renata Lewandovska, product manager for spectral

spectroscopic techniques. Designed to make labs

applications at Digital Surf, added, “We’re very

more efficient, in a single interface it features:

excited to collaborate with Wiley and to bring a stand-alone software product for complete spectral

•

Spectral processing and analysis

•

Spectral map and image processing

•

Correlative analysis

Wiley

•

3D visualisation of 2D compositional data

microscopic

analysis to the users of their innovative solutions.”

Surface-to-Spectral images

from

fluorescence,

Analysis

supports

Raman, TERS, IR,

Users can even take their analysis a step further

nanoIR,

by sending spectra to Wiley’s KnowItAll software*

cathodoluminescence, EDX/EDS and XPS, so

photoluminescence,

to search against spectral libraries for further

even when switching between instruments or

investigation.

microscopes, analysis workflow remains intact.

Graeme Whitley, Director of Data Science

https://sciencesolutions.wiley.com/

Solutions at Wiley, highlighted the value, “Being able

wiley-surface-to-spectral-analysis/

99

NEW PRODUCTS

Introducing the Quantum Diamond Microscope from Quantum Catalyzer The NEW Quantum Diamond Microscope (QDM) is a premier imaging tool based on nitrogen vacancy (NV) centres in diamond — providing non-invasive magnetic imaging with high spatial resolution and wide field-of-view. And it’s available through Quantum Design UK and Ireland.

Developed in the labs of QDM.IO co-founders Roger Fu and Ronald Walsworth, the QDM enables widefield imaging of magnetic fields, with applications spanning geoscience, bio-imaging, electronics, materials characterisation, and quantum research.

Features: Image millitesla to nanotesla magnetic fields

Tuneable spatial resolution down to less than one micron and field-of-view up to four millimetres in a single image. Larger samples can be readily mapped by tiling multiple images.

Correlate Magnetic and Optical Images

Collect magnetic and optical images of samples using the same optical system for straightforward coregistration.

Vector Measurements

The diamond sensor enables reconstruction of the

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ISSUE 76 DECEMBER 2024

magnitude and direction of magnetic fields, providing superior reconstruction of magnetic source distributions.

Quantum-Grade Diamond

Manufactured by QDM.IO partner Element Six, with properties optimised for microscale magnetic field mapping applications.

Robust and Easy to Use

Operates with no cryogenics, vacuum systems, special infrastructure, or power requirements.

Applications Biomagnetism Photovoltaics Electronic Components The QDM has unlocked deeper understanding of our terrestrial world and solar system, rapidly becoming a valuable tool in remanent magnetisation studies of geological samples. As an example, magnetic imaging of magnetic grains in 4-billion-year-old zircons and meteorites has better constrained our understanding of the magnetic geodynamo of both Earth and Mars. QDM analysis of modern speleothems has also enabled more reliable interpretation of a new paleoclimate proxy. www.qd-uki.co.uk

abberior launches next-level deconvolution software Modern deconvolution software has limitations: to

any assumptions about the sample’s properties and

deal with noise and background, it relies on a-priori

without introducing artifacts.

assumptions about the sample structure that are frequently inaccurate and may therefore produce artifacts. abberior

Another challenge is background removal. In every recorded image, signal and background are mixed, and standard deconvolution algorithms cannot fully

now

launched TRUESHARP

image

boosting, a deconvolution software that resolves this shortcoming. By incorporating information about noise and background, it reliably removes these disturbances without falsifying the images and increases resolution.

distinguish between the two.

TRUESHARP solves this problem by analysing signal and background separately. It has three ways to identify background: it can apply an estimation algorithm to separate background from structure. Or, even better, TRUESHARP can work

Dealing with noise in post-processing is not trivial.

in information that was physically measured with

Standard procedures tend to amplify noise, and

abberior’s MATRIX array detection and TIMEBOW

countering this with regularisation means making

lifetime imaging.

assumptions about the sample structure. Proceeding from this guesswork, the algorithm tries to remove noise. The resulting image may look good. However, the sample may not meet the assumptions and, as a consequence, processing pushes the result in the wrong direction, generating undetectable artifacts.

Lifetime data recorded with TIMEBOW allows to e.g. separate autofluorescence background or lowresolution STED data based on different lifetimes.

The MATRIX detector picks up signal from different angles simultaneously and in this way is able to differentiate between background and in-

TRUESHARP takes a different approach. It makes

focus signal.

use of a simple physical fact: noise is random.

https://abberior.rocks/superresolutionconfocal-systems/modules/truesharpdeconvolution/

TRUESHARP identifies noise by its randomness and separates it from the structure’s signal. This way, it can reliably remove noise without making

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NEW PRODUCTS

Enhancing Widefield Fluorescence with 4-channel LED Illumination LED Illumination has become the go-to choice

Optimised for live cells – Achieve precise

for widefield fluorescence microscopy, but it’s not

control with 0-100% intensity modulation and

always easy to choose the right light source when

individual channel switching, all designed to

retrofitting or choosing a new microscope setup.

minimise photodamage and capture dynamic events

CoolLED can help simplify this decision with the four-channel pE-400max. Designed as the best all-

a manual pod.

rounder, it has four powerful LEDs covering DAPI

Fast multi-colour imaging – Capture more

through YFP to Cy5 (365-635 nm), and here are just

data points faster, thanks to high-speed TTL

a few advantages:

triggering and Pinkel filter sets, with the option to

Enhanced image clarity – Intense, stable

house excitation filters at each LED.

illumination delivers clear and detailed images even

For simple lamp replacements, the white light pE-

in the most demanding applications.

400 offers identical LEDs to the pE-400max and is

Flexible fluorophore choice – Compatibility

ideal for providing widefield capability on confocal

with all popular fluorophores from DAPI to Cy5

102

in real time. Control options include TTL, USB, and

setups.

(including enhanced YFP coverage) suits a range of

www.coolled.com/products/pe-400-

experiments now and in the future.

series

ISSUE 76 DECEMBER 2024

High-throughput 3D imaging with the UltraMicroscope Blaze™: Stain, clear, and image up to 48 organoids, 12 xenografts, or 8 whole mouse brains in one go The UltraMicroscope Blaze is renowned for its full automation and spacious chamber size, making it ideal for imaging multiple samples. With the high-speed LightSpeed Mode, imaging on the UltraMicroscope Blaze is now faster than ever.

With the new MACS® UltraMounts, the latest release from the expert imaging engineers at Miltenyi Biotec, harness the full power of the

MACS UltraMounts and the UltraMicroscope Blaze!

Your samples can be visualised as a single image file or segregated by individual wells as independent image files. As always, you can transfer your image files into MACS iQ View 3D to utilise the software’s batch image processing for downstream image stitching and 3D deconvolution with just a click of a button!

Watch videos showcasing this potential:

UltraMicroscope Blaze. You can now image up to

MACS®

48 organoids or 12 xenografts in a single run. Their

imaged in 3D with the UltraMicroscope Blaze™

ingenious design enables you to perform tissue

Eight

labelling and clearing while your samples are loaded

UltraMicroscope Blaze™ and MACS® UltraMount

into the holders, so you can batch both tissue

8 Sample Holder

clearing and imaging into one easy workflow. Bring

www.miltenyibiotec.com

high-throughput imaging into your lab with the new

UltraMount adult

mouse

48

organoids

brains

imaged

holder with

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NEW PRODUCTS

MACS® iQ View – 3D Large Volume: Light sheet microscopy image processing software – unlocking superior quality with just a few clicks MACS iQ View – 3D Large Volume is a user-friendly

approach ensures ease of operation and eliminates

light sheet microscopy image processing software

the need for manual intervention at every stage.

tailored for managing, stitching, and processing

Batch processing

large 3D datasets captured by the UltraMicroscope Blaze™. It empowers you to gain meaningful insights

The software supports batch processing, allowing

and enhance image quality with ease. Its user-friendly

users to queue and initiate various workflows across

interface simplifies navigation and operation, making

multiple datasets. This feature proves especially

it accessible to users of all skill levels.

valuable when dealing with extensive datasets and

Effortless and streamlined processing workflow processing

modules

optimised

for

the

Compatible output file

UltraMicroscope Blaze that can be used to perform

The output data is presented in the widely

a variety of tasks, including 3D cropping, destriping,

compatible .ome TIFF format, ensuring seamless

denoising, deconvolution, stitching, and contrast

integration with a variety of imaging analysis

compression.

software.

The image processing workflow facilitates the

For more information visit our website.

straightforward assignment of processing modules

www.miltenyibiotec.com

in a proposed step-by-step sequence, enabling automatic execution of each step. This streamlined

104

Blaze, particularly in the LightSpeed Mode, ensuring a smooth processing workflow.

The software includes a comprehensive suite of

imaging multiple samples using the UltraMicroscope

ISSUE 76 DECEMBER 2024

LiveCodim has a new algorithm!

Our software team in Paris, working with Prof. Lionel

focal plane and light captured from samples in the

Moisan from Université Paris Cité, has successfully

focal plane. The structures reconstructed using the

completed a new imaging algorithm called H3. We

H3 algorithm, shown on the image on the right

now have two methods to calculate the image

below, are significantly sharper than when using the

from the measured data from the instrument,

original Nesterov algorithm (left, below). LiveCodim

which allow us to achieve even better results. This

is now available in the UK, contact us for more info!

algorithm enables us to distinguish more accurately

www.telight.eu

between scattered light emitted from outside the NESTEROV

H3

Fibroblast sample: violet= Actin, cyan= microtubules, yellow=mitochondria

If you would like your new product information to appear on these pages, contact infocus Magazine at advertising@infocus.org.uk The announcements in this Section are compiled by the manufacturers. They in no way represent a recommendation by the Royal Microscopical Society for any particular instrument or equipment. The Royal Microscopical Society does not endorse, support, recommend or verify the information provided on these pages.

105

RMS Ambassador Rob Kesseler captures the wonder of seeds in his latest book Seeds Time capsules of life

By Rob Kesseler & Wolfgang Stuppy Hardback ISBN: 978-1-906506-75-9 A fascinating new book co-authored by RMS

The book presents a comprehensive natural

Ambassador Rob Kesseler captures the artistic and

history of seeds, illustrated with stunning close-up

scientific wonder of seeds – at a microscopic level.

photographs and scanning electron micrographs

Rob, who is a renowned visual artist and Emeritus Professor of Arts, Design & Science at Central Saint

revealing the beauty and sophistication of some of the tiniest examples.

Martins in London, has published a new edition

The origins of seeds are traced back 360 million

of Seeds: Time Capsules of Life, an eye-catching

years, with Rob and Wolfgang examining how

collaboration with seed morphologist Dr Wolfgang

they evolved into highly sophisticated structures

Stuppy.

that have enabled plants to colonise the world -

Rob and Wolfgang take the reader on a captivating journey into the microcosm of seeds, where art and science converge to unveil one of nature’s most stunning secrets.

conquering almost every habitat from the Antarctic to the hottest deserts. It explores the role of seeds as ‘time capsules’ of new life - sometimes travelling thousands of miles and waiting many years before germinating to bring forth a new plant.

Examples in the book range from the giant Seychelles nut that weighs twenty kilos to the tiny dust-like seeds of orchids. They also include the mesmerising blue seeds of the Malagasy Traveller’s Tree, the perfectly aerodynamic, wafer-thin gliders of the Monkey Pod and, perhaps most extraordinarily, the seeds of the parasitic Desert Hyacinth

that

resemble

a

miniature honeycomb.

The front cover of Seeds:Time capsules of life features the Caiophora arechavaletae (Loasaceae) – native from Brazil to Uruguay – balloon seed displaying the most extreme form of the typical honeycomb pattern found in wind-dispersed seeds.

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ISSUE 76 DECEMBER 2024

Double-page spread from the book showing (left) the tree medick fruit, (Medicago arborea - Fabaceae) viewed from the bottom end; and (right) the blackdisk medic (Medicago arbicularis – Fabaceae) also viewed from the bottom end. Both are native to the Mediterranean.

This book not only captivates and enlightens those

upon joining the Royal Botanic Gardens, Kew in

interested in the natural world, but also anyone

1999. In 2002, he transitioned to Kew’s Millennium

drawing inspiration from the wonderful and

Seed Bank at Wakehurst, dedicating fifteen years

endlessly fascinating world we live in.

to the meticulous study of seeds from all over the

A fascinating talk about their work, given by Rob and Wolfgang to the Tree Council, is available to view on Youtube.

world. He currently holds the position of curator of the Botanic Garden at Ruhr-University in Bochum, Germany.

About the authors: For the past twenty years, Rob Kesseler has worked with botanical scientists and molecular biologists around the world to explore the living world at a microscopic level. Using a range of complex microscopy processes, he creates intense, large format photographs that extend the traditions of botanical art into a contemporary field.

He has a long association with the RMS as an ambassador for the Society, and gave a plenary talk at mmc2021 on The use of Energy Dispersive X-ray Spectrometry (EDS) and Scanning Electron Microscopy (SEM) to examine pollutant particles on leaf surfaces.

Wolfgang Stuppy is a globally recognised seed specialist. He began his career in plant conservation

Rob Kesseler.

107

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Innovation with Integrity

R E P O RT

A look back at FlowCytometryUK 2023 16 November, Cambridge, UK

T

he

Royal

Microscopical

Society

Robinson gave a stimulating, if mind-perplexing,

FlowcytometryUK 2023 meeting welcomed

talk on the concept of Quantum Flow cytometry;

delegates to the Babraham Institute in

proposing that we have reached the bounds of

Cambridge in November. As the first in-person

spectral flow technology, and that in order to

meeting since the pandemic, it was exciting to be

expand to more parameters, we need to develop

together again for this productive meeting, with

the technology to detect a different unit than light,

delegates from across the country enjoying insightful

coined “Quantum Flow Cytometers”, the next

talks which sparked stimulating discussion.

generation of spectral cytometers. This would

RMS Honorary Fellowship: J Paul Robinson The meeting was also special in that it saw Professor Paul Robinson welcomed as an RMS Honorary fellow.

Robinson, Distinguished Professor of Cytometry at Purdue University, has been immensely influential to the flow cytometry research we do today. The

include advanced laser technology, new detectors, and bandwidth diffraction elements, leaving delegates contemplating the future of the Cytometry field.

The RMS Flow Cytometry Section Medal winner Christopher Hall Christopher Hall was honoured with an RMS Flow

application of some of his work was much discussed

Cytometry Section Medal and gave an inspiring

at this meeting as he was a member of the Purdue

talk on his career journey. He has made a great

University engineering team that invented spectral

contribution to the teaching of flow cytometry

flow cytometry.

in the community, through societies, educational resources and open-source scripts and analysis workflows. Indeed, I have benefitted personally from his expertise and willingness to help; without his input my own work would have progressed far more slowly (if at all).

From AI and automation to non-traditional flow cytometry applications With speakers from many disciplines, the meeting showcased the variety of applications to which flow cytometry can be used. The powerful technology of flow cytometry is often thought of as only useful for Immunological-based research; the talks throughout J Paul Robinson signs the book of RMS Honorary Fellowship as RMS President Peter O'Toole looks on.

the day challenged this misconception, with speakers

109

Christopher Hall receiving his award from former RMS Flow Cytometry Section Chair, Karen Hogg.

highlighting research from protein homeostasis,

which would normally take 2-3 hours, in just 20

marine biology and the study of microplastics.

minutes! Emphasis was also placed on the teaching

A running theme throughout the meeting was the need for flow cytometry processes to evolve in line with the rapid growth of panels. Bench side delegates were excited by technologies which

streamline the analysis and interpretation of flow cytometry data, with its increased parameters and complexity.

automate the generation of antibody cocktails,

Overall, the event brought together cytometry

saving time and eliminating user error. For example,

enthusiasts and experts in person again with great

the I.DOT can prepare a 25-colour panel including

success, and the Flow CytometryUK 2025 meeting

full stain, FMOs, and single stain cells and beads,

will be held at the University of Newcastle.

Delegates enjoying some 'break-out' time during the event.

110

of the data packages and algorithms developed to

ISSUE 76 DECEMBER 2024

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Submission Guidelines

infocus is the Royal Microscopical Society’s (RMS) vibrant and striking quarterly magazine for members. It provides a common forum for scientists & technologists who use any form of microscope, including all branches of microscopy. Published four times a year, infocus is free to members of the RMS. infocus features articles on microscopy related topics, techniques and developments, an events calendar, news, event reports, book reviews, new product information, and much more. infocus welcomes submissions of: Articles - Full articles or reviews of general interest to microscopists, of approximately 30004000 words (excluding references), with images/ figures (as many as appropriate, 4-8 as a guide).

Longer articles can also be considered.

Short Articles - Short topical articles, review articles or articles providing hands-on help for microscopy methods.

Primer Articles - Short general articles that are focussed on specific techniques.

Debuts - Student articles publishing emerging results from a project. Results may still be incomplete, but areas of progress/problems should be highlighted, with the aim of provoking feedback.

Book Reviews – if you are a member of the RMS and are interested in writing book reviews for infocus, please contact Owen Morton owen@rms.org.uk.

Please see recent issues of infocus for examples of articles and reviews. To request a sample copy of infocus contact owen@rms.org.uk If you are interested in submitting to infocus, contact: editor@infocus.org.ukj

Article Text

• Abbreviations should be used sparingly and only if a lengthy name/expression is repeated throughout the article. When used, the abbreviated name or expression should be cited in full at first usage, followed by the abbreviation in parentheses.

• Authors should provide a photograph, brief biography as well as contact information that will be published.

References

References in the text should be in the form Joy (2000) or Joy & Williams (2000). For three or more authors, use the form Echlin et al. (2000). The reference list should: • be listed in alphabetical order of first authors’ surnames.

• (where a journal is cited) - include authors’ surnames and initials, date of publication, title of paper, name of journal, volume number, and first and last page numbers.

• (where a book is cited) - include authors’ surnames and initials, title of book, year of publication, edition, followed by publisher and town, county/state (and country if necessary) of publication.

• (where a URL is cited) – include authors’ surnames and initials, year of publication, title of page, URL and date accessed.

Images / Figures • Figures can be one column/half page width, 65.5 mm or two column/full page width, 135 mm.

• Larger images may fill the page/spread. A full page of the magazine is 170 x 250 mm, a double page is 340 x 250 mm.

• Text in figures (labels, axis labels, legends, etc) should be Helvetica or Arial, 8pt size.

• Figure and table captions should be listed numerically at the end of the article text

• Text should be in a standard font (e.g. Times New Roman or Arial) at a size of 12 pt.

• Line weights and line strokes should have a maximum value of 1 and a minimum of 0.25.

• Articles should begin with a brief summary, which accurately summarises the content and is intelligible without reference to the text.

• For graphs and plots, whenever possible, please submit vectorized images.

• As much as possible, please avoid white spaces.

• Footnotes and appendices should not be used unless absolutely necessary.

• All images must be high resolution – 300dpi or more.

• The hierarchy of headings within the text should be clear.

• Submission files should be in CMYK format and can be supplied as tiff, jpeg or eps files.

• Spelling should conform with The Concise Oxford Dictionary and SI units must be used.

• Images MUST include scale bars or field widths where relevant.

Double page of magazine, 340 x 250mm (Trim size) 112

ISSUE 76 DECEMBER 2024

• Total number of images/figures/tables should not exceed 15 including tables.

Proofs

Prior to publication, authors will be sent a PDF of the article by email for approval.

Authors should ensure articles are thoroughly checked before submission – proof amendments should be limited to minor corrections only.

Offprints Five hard copies of the issue in which the article is published will be sent to the author, together with an emailed PDF of the article.

Copyright Authors are requested to assign copyright to the RMS. However, authors may make copies of their own articles without seeking permission from the RMS, provided that such copies are for free distribution only (they must not be sold) and provided that infocus is properly acknowledged (issue number, month and page number should be given). Permission to reproduce material from infocus in other publications will not be given to third parties except with the consent of the authors concerned.

Authors are responsible for obtaining permission to reproduce copyright material from other sources.

Approval for reproduction/modification of any material (including figures and tables) published elsewhere should be obtained by the authors before submission of the manuscript and the source of the material should be properly acknowledged. Authors are responsible for any copyright fee involved.

One column/half page width, 65.5mm Figure 1. Width of figure or table confined to one column.

Authors are requested to complete and submit a signed copy of our copyright sign-off form. This is available on the RMS website (www.infocus.org.uk).

Two column/full page width, 135mm

Figure 2. Width of figure or table spanning full width of page.

113

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