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Martin Jones

@martinjones.bsky.social
2.5K followers 1.9K following 49 posts

Ex-physicist in a biology institute, working on image analysis and building new hardware at the Francis Crick Institute ORCID: 0000-0003-0994-5652

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Reposted by Martin Jones
napari @napari.fosstodon.org.ap.brid.gy · 26/09/2026
🚀 napari is hiring Remote Developers-in-Residence! Join us to build the future of interactive n-dimensional data visualization in Python. 💻 60% Dev / 20% Maintenance / 20% Community & Outreach 💰 $59.50/hr (Contract, 14–35 hrs/wk) 🌍 100% Remote, open globally Learn more and apply today […]
fosstodon.org
Original post on fosstodon.org
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DrLachie @drlachie.bsky.social · 10/09/2026
Proud to present the publication of napari-lattice – our solution to the immense computational requirements of Lattice Light Sheet and Oblique Plane Microscopy. onlinelibrary.wiley.com/doi/10.1111/... Before I get into the thread, the important part is on github: github.com/BioimageAnal... (1/n)
onlinelibrary.wiley.com
napari‐lattice: A user‐friendly image processing tool for lattice light‐sheet microscopy data
Lattice light-sheet microscopy (LLSM) enables researchers to capture high-speed 3D videos of living cells with high definition and minimal damage. However, this technology generates terabytes of data....
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Di Jiang @dijiang319.bsky.social · 09/07/2026
In print today @science.org Laser phase plate improves structure determination of small proteins by cryo-EM | Science www.science.org/doi/10.1126/...
science.org
Laser phase plate improves structure determination of small proteins by cryo-EM
Phase plates can, in principle, overcome the poor image contrast in cryo–electron microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. However, previous de...
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Martin Jones @martinjones.bsky.social · 06/05/2026
Do people keep talking to you about "notebooks", and now you've left it too long to ask what on earth they are?! Then check out Piper's talk in the @ccp-volumeem.bsky.social #ShowAndTell series! Going from the basics, through to tips and tricks and more advanced topics #BioImageAnalysis #VolumeEM
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CCP-volumeEM @ccp-volumeem.bsky.social · 05/05/2026
Missed our April Show & Tell? Watch Dr Piper Fowler-Wright’s talk, “Jupyter Notebooks for Shareable Research Outputs” : a practical introduction to using notebooks for reproducible, well-documented research 🧪 🎥 www.youtube.com/watch?v=wzh4...
youtube.com
Jupyter Notebooks for Shareable Research Outputs with Dr Piper Fowler-Wright
YouTube video by CCP-volumeEM
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Reposted by Martin Jones
CCP-volumeEM @ccp-volumeem.bsky.social · 06/05/2026
Join our next CCP-volumeEM Show & Tell webinar! 'OME-Zarr: A Next Generation File Format for FAIR bioimaging data' with Chris Barnes 📅 Tuesday 19 May, 12:30pm BST 💻 60-minute online talk You can register here: crick.zoom.us/webinar/regi...
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Andrew G. York @andrewgyork.bsky.social · 29/04/2026
Meet MagLuc: a magnetically-controlled luminescent protein. This is a foundational tool for remote control of biological processes, also known as "magnetogenetics". Can you tell when the magnetic field turns on and off? From @mariaingaramo.bsky.social and the team at @nonfictionlabs.bsky.social
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Helena Watson @helenawatson.bsky.social · 25/04/2026
Preprint 🧵! I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition! BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a www.biorxiv.org/content/10.6... (1/6)
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 10/04/2026
⏳️ Have you registered yet? #EuroBioImaging's Image Data Community Days event is happening next week. If you're curious about biological & preclinical #imagedata analysis, management, tools & more this event is for you. Registration is FREE & open to all⤵️ www.eurobioimaging.eu/events/image...
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Crick BioImage Analysis Symposium @cbias.bsky.social · 09/04/2026
🚨🔬🚨🔬🚨 We are pleased to announce that registration for the 7th edition of the Crick BioImage Analysis Symposium #CBIAS 2026 is now open! 🕐November 23rd-24th, 2026📍The Francis Crick Institute, London. We look forward to seeing as many of you as possible there (or online 😀)
crick.ac.uk
Crick BioImage Analysis Symposium 2026
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 10/04/2026
Analyse public OME‑Zarr images using models from the BioImage Model Zoo! 🦒 Join us April 16 🕐️ 13:00–15:00 CEST — a perfect fit for Python 🐍 users ready for hands‑on work. @ai4life.bsky.social #OMEZarr #AIinScience #ImageAnalysis #Workshop forms.gle/5hQh1BoACPaF...
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CCP-volumeEM @ccp-volumeem.bsky.social · 25/03/2026
Missed our latest CCP-volumeEM Show and Tell webinar? Dr Kimberly Meechan’s talk on Good practices for image analysis software is now available to watch on YouTube: www.youtube.com/watch?v=HHJJ...
youtube.com
Good practices for image analysis software with Dr Kimberly Meechan
YouTube video by CCP-volumeEM
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Joel Lüthi @joelluethi.bsky.social · 26/03/2026
🔬 Next Open Bioimaging Practices Meetup (OBPM) – Mar 31, 16:00 CET Hybrid: FMI Basel & Zoom Talk by @jo-soltwedel.bsky.social : Transforming OME-Zarr: What’s coming in v0.6 Plus short updates from the BVC & time for discussion www.biovisioncenter.uzh.ch/en/events/Up...
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup: March 2026
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Martin Jones @martinjones.bsky.social · 25/03/2026
Dominik Kutra from @ilastik-team.bsky.social presenting the latest updates to #ilastik for #BioImageAnalysis at the @zeiss-microscopy.bsky.social "From 3D Light to 3D Electron Microscopy“ symposium at @crick.ac.uk - very brave live demo with TB scale data! @em-stp.bsky.social #VolumeEM
A male researcher standing on stage in front of a large presentation screen with the text "ALL GOOD!??" showingA male presenter on stage in front of a screen showing electron microscopy image data, with colourful overlays denoting a segmentation
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Brandy A Freitas @brandy-syglass.bsky.social · 12/03/2026
Streaming OME-Zarr data directly into syGlass for #3DThursday🌍🔬 With #syGlass v2.6.0, datasets can stream from disk, S3, or HTTPS with no massive downloads required. Huge thanks to the community building open imaging standards: @openmicroscopy.org #OMEZarr #Microscopy #OpenScience #Bioimaging
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Martin Jones @martinjones.bsky.social · 17/03/2026
Enjoying @k-meech.bsky.social's #ShowAndTell talk in the @ccp-volumeem.bsky.social series while on holiday, with suitable holiday lunch 😄 The talk will be uploaded to the #CCPvolumeEM YouTube channel, link from the website: www.ccp-volumeem.ac.uk/showandtell #BioImageAnalysis #CoSeC #VolumeEM
View of a laptop on a small table, with a plate of scones with jam and clotted cream and a cup of tea next to it
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Royal Microscopical Society @royalmicrosoc.bsky.social · 17/03/2026
Just a few days left to submit your abstract for the 21st International Microscopy Congress #IMC21 - Deadline *THIS FRIDAY* (20th March) Don't miss the chance to share your work with the global #microscopy community in Liverpool this summer! 🙂 🔬 Abstract submissions: ow.ly/sknS50Yv9pk
Liverpool waterfront at sunset with historic buildings promoting the 21st International Microscopy Congress in 2026.
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Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 15/03/2026
Are FMs actually FMing? ⛓️🔬 Thrilled to share that our paper on Foundational Models for mitochondria segmentation in EM is heading to the @iclr-conf.bsky.social 2026 LMRL Workshop! 🚀 Check out the full work here: 📄 ArXiv: arxiv.org/abs/2602.08505 📄 OpenReview: openreview.net/forum?id=Bba...
arxiv.org
Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Although vision foundation models (VFMs) are increasingly reused for biomedical image analysis, it remains unclear whether the latent representations they provide are general enough to support effecti...
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David Stansby @dstansby.bsky.social · 13/03/2026
The paper that sums up what I've been working on and running for the last three years was published this week 🎉 www.science.org/doi/10.1126/...
science.org
The Human Organ Atlas
The Human Organ Atlas provides open access to 3D images of human anatomy spanning whole organs to cellular scale resolution.
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Daniel Krentzel @danielkrentzel.bsky.social · 24/02/2026
Our preprint outlining a deep learning-based phenotypic screening approach for the discovery of new TB drugs is out on bioRxiv now 💊🦠 🔗 doi.org/10.64898/202... Thank you @awehenkel.bsky.social @chzimmer.bsky.social @spetrella.bsky.social @curieuseny.bsky.social and everyone else not on bsky (yet)🙏
Screenshot of the title and author list of the preprint entitled "Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria"
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CCP-volumeEM @ccp-volumeem.bsky.social · 12/03/2026
Our first #CCPvolumeEM #hackathon is underway, with some amazing merch! We're looking at building community resources and knowledge for the use of #NGFF in #volumeEM #BioImageAnalysis #OMEZarr #OMENGFF @cosec-ukri.bsky.social
View of the back of a laptop with a holographic sticker saying "CCP-volumeEM". In the background, out of focus, are a group of people sat at desks
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Virginie Uhlmann @virginieuhlmann.bsky.social · 10/03/2026
If you've been wondering what our current obsession with OME-Zarr and lego blocks is about, I have good news for you: the Fractal preprint is out! Thanks to @joelluethi.bsky.social , all co-authors, and the Fractal developers and users community for making this beautiful project a reality ❤️
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CCP-volumeEM @ccp-volumeem.bsky.social · 10/03/2026
Looking forward to learning more about this and how it can be used for #volumeEM at the #CCPvolumeEM #NGFF hackathon at @ebi.embl.org this week! #BioImageAnalysis @cosec-ukri.bsky.social #OMEZarr
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Joel Lüthi @joelluethi.bsky.social · 10/03/2026
We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10🧵) www.biorxiv.org/content/10.6...
biorxiv.org
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Erick Ratamero @erickratamero.com · 10/03/2026
Calling all OME Community members, contributors, and lurkers! Please take a minute to answer the OME 2026 Community Survey (docs.google.com/forms/d/e/1F...) to help us prepare for discussing the future of OME governance during the OME 2026 Community Meeting at the end of April.
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VolumeEM @volumeem1.bsky.social · 09/03/2026
New Web Page - Volume EM Industrial Partners www.volumeem.org/industrial-p... We’re excited to introduce our newly curated Industrial Partners page, showcasing organizations recognized by the volumeEM Community as key contributors in the field.
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Martin Jones @martinjones.bsky.social · 09/03/2026
Including a piece by Jenny Hounsome, @h-spiers.bsky.social, @em-stp.bsky.social and me on some @crick.ac.uk outreach we've been doing over the past few years with local primary schools
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BioImagingUK @bioimaginguk.bsky.social · 06/03/2026
📢 UK RESEARCHERS - Ever wished you could try a completely different imaging approach on your sample but lacked access to equipment or funds? That's exactly what the Euro-BioImaging UK Node User Access Fund is for! Applications are open year-round, with 3 deadlines/yr: 📅 31 Mar | 31 July | 30 Nov
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Martin Weigert @maweigert.bsky.social · 02/03/2026
Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context. Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social
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Marie Held @makaefer.bsky.social · 25/02/2026
Woohoo! So looking forward to the next iteration. 🤩
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Stefania Marcotti @lankylaste.bsky.social · 27/02/2026
Save the date! We’re back at the @crick.ac.uk next November!
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Crick BioImage Analysis Symposium @cbias.bsky.social · 25/02/2026
📣We’re back 🔬👀🖥️! #CBIAS2026 returns 23–24 November 2026: Join the bioimage analysis community to discuss advances in quantitative imaging & computational methods for image analysis. Great opportunity for early-career analysts & microscopists to present and connect. #CBIAS2026 #BioimageAnalysis
crick.ac.uk
Crick BioImage Analysis Symposium 2026
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CCP-volumeEM @ccp-volumeem.bsky.social · 02/03/2026
Our first 'Show & Tell Series' webinar, presented last week, is now available on YouTube. Watch here: www.youtube.com/watch?v=E-pi... We hope it’s useful to the community - please share with anyone who may be interested #VolumeEM #Bioimaging
youtube.com
A brief introduction to the use of containers for reproducible image analysis with Dr Martin Jones
YouTube video by CCP-volumeEM
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CCP-volumeEM @ccp-volumeem.bsky.social · 26/02/2026
An important focus of @cosec-ukri.bsky.social activities like #CCPvolumeEM and other CCPs is the environmental impact of scientific computing. @epcc.bsky.social have teaching materials at epcced.github.io/2026-02-26_G... Comic image from xkcd.com/1379/ #GreenHPC #GreenComputing
A comic from the XKCD webcomic showing the effects of CO2 emissions, with a temperature scale indicating the effect of temperature changing in 4.5 degree centigrade steps, from an ice age 20,000 years ago to possible future scenarios.
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The Francis Crick Institute @crick.ac.uk · 25/02/2026
Thanks to His Royal Highness Prince William for visiting the Crick today to explore how education, research and innovation are helping to deliver benefits in the UK and across the world – from antimicrobial resistance to the biology underlying our mental health. 🔗 www.crick.ac.uk/news/2026-02...
His Royal Highness Prince William is talking with Edith Heard, who is to his left, inside a well-lit building entrance. They are both smiling and walking towards the camera.His Royal Highness Prince William Is sitting at a round table with a group of students. They are all wearing safety glasses, and he is holding a pipette. There is a variety of scientific instruments in the middle of the table. His Royal Highness Prince William is sitting in front of a microscope wearing a lab coat. He is laughing while looking towards someone to his left, also in a lab coat. They are both inside a large white room.His Royal Highness Prince William stands next two Edith heard, both with  arms folded across their front. He is facing and talking to three other people inside a well-lit building entrance.
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Dave Barry @david-j-barry.bsky.social · 13/02/2026
Do you do image analysis? Want to make it more robust and reproducible? Have you heard of containers, but don't know why they’re useful, and how to use them? @martinjones.bsky.social will explain all: crick.zoom.us/webinar/regi...
crick.zoom.us
Welcome! You are invited to join a webinar: CCP-volumeEM Show and Tell - February 2026. After registering, you will receive a confirmation email about joining the webinar.
'A brief introduction to the use of containers for reproducible image analysis' with Dr Martin Jones Abstract: Reproducibility of scientific data analysis is critical, but can be particularly challe...
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 11/02/2026
💖 We join #LoveDataWeek2026 by sharing the recordings from Image Data Community Days 2025! Follow the “Where’s the data?” theme with on-demand sessions on FAIR principles, analysis tools, AI & preclinical imaging. 🎬 Watch anytime here youtube.com/playlist?lis...
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Peter O'Toole @yorkbioimaging.bsky.social · 03/02/2026
Unleashing live-cell imaging for the masses! Adapting the OpenFlexure Microscope for Affordable Live-Cell Imaging www.biorxiv.org/content/10.6... Fits into existing incubators for time-lapse experiments & feeds into existing bioimaging analysis pipelines. Thanks @wellcometrust.bsky.social funding
image of the OpenFlexure Microscope on the left. On the right, our adapted live-cell imaging openflexure microscope with cradle to negate vibrations inside an existing incubator
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The Francis Crick Institute @crick.ac.uk · 05/02/2026
New research from the Crick and @umontreal.ca has found the missing link between two chemical pathways that control blood vessel branching, potentially opening the door for new treatments for a currently incurable genetic bleeding disorder. www.crick.ac.uk/news/2026-02...
crick.ac.uk
‘Missing link’ protein key to restoring disorganised blood vessels
Understanding how the body maintains the balance between blood vessel formation and stabilisation could help treat blood vessel disorders, cancer and prevalent eye diseases.
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BioImagingUK @bioimaginguk.bsky.social · 02/02/2026
🔬UK researchers: Access cutting-edge bioimaging tech + expert support with our User Access Fund! 💷 £5k for imaging 💷 £2k for image analysis Choose from 6 top UK facilities, contact them, then apply! rms.org.uk/user-access-fund ⏰ Next deadline: 31 March ✅ Decision in 4 weeks Pls share!
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Séamus Holden 🔬🦠🧫 @seamusholden.bsky.social · 02/02/2026
iCASE PhD project available in my lab, combining microscopy method development with high throughput screening of bacteria. Applications to antibiotic drug discovery and screening for new cell division proteins. Collaboration with Cairn Research #microsky #bioimaging www.findaphd.com/phds/project...
findaphd.com
Image-based bacterial phenotyping and antimicrobial drug discovery using smart high-throughput super-resolution microscopy at University of Warwick on FindAPhD.com
PhD Project - Image-based bacterial phenotyping and antimicrobial drug discovery using smart high-throughput super-resolution microscopy at University of Warwick, listed on FindAPhD.com
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Crick Light Microscopy @calm-stp.bsky.social · 19/01/2026
We Are hiring!! 👨‍💻👩‍💻 CALM's new Data and Systems Steward Role is live 🎉https://crick.wd3.myworkdayjobs.com/External/job/London/Data-and-Systems-Steward_R2551 closing date 8th Feb!
crick.wd3.myworkdayjobs.com
Data and Systems Steward
Salary for this Role: From £43,630 with benefits, subject to skills and experience. Job Title: Data and Systems Steward Reports to: Kurt Anderson Closing Date: 08/Feb/2026 23.59 GMT Job Description: D...
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Crick Image Analysis Team @crick-ia-team.bsky.social · 27/01/2026
We are hosting an #Ilastik workshop on March 27th, led by Dominik Kutra, senior research software engineer @ilastik-team.bsky.social The course is open to students and staff at @crick.ac.uk and partner universities (@ucl.ac.uk, @kingscollegelondon.bsky.social and @imperialcollegeldn.bsky.social)
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Crick BioImage Analysis Symposium @cbias.bsky.social · 13/01/2026
Three of our early career participants wrote about their experiences at #CBIAS2025 on @focalplane.bsky.social. Check out the blog post!
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Crick BioImage Analysis Symposium @cbias.bsky.social · 05/01/2026
The #CBIAS2025 poster collection is now available, along with associated DOIs for further dissemination. Take a look! crick.figshare.com/collections/...
crick.figshare.com
Crick BioImage Analysis Symposium 2025 Posters
CBIAS features a mix of invited and selected talks, poster sessions, and panel discussions focused on current topics in image analysis and image processing for microscopy and computational microscopy....
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Crick BioImage Analysis Symposium @cbias.bsky.social · 28/01/2026
Another brilliant #CBIAS2025 review is out, thanks to Virginia Silio, scientific ambassador for @eurobioimaging.bsky.social and Imaging Specialist at the Centre for Molecular & Cell Dynamics @ucl.ac.uk! www.eurobioimaging.eu/news/exchang...
eurobioimaging.eu
Exchanging with the BioImage Analysis Community
On November 24-25 2025, Euro-BioImaging Scientific Ambassador, Virginia Silio, attended the Crick BioImage Analysis Symposium (CBIAS) 2025, held in London. The two-day event brought together around…
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Stratocore @stratocore.bsky.social · 15/01/2026
🔬 EMUKI 2026 is coming up Stratocore will be sponsoring & attending EMUKI 2026 in Dublin on 12–13 Feb, bringing together the #electronmicroscopy community to discuss facility management, technical innovation and career pathways. 🔗 f.mtr.cool/xwgppvqkeu @royalmicrosoc.bsky.social
f.mtr.cool
EM-UKI 2026
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 meeting will include techno bites, talks, and discussions, and also hosts the annual RMS EM lecture.
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FocalPlane @focalplane.bsky.social · 13/01/2026
Jacqueline Chalakova, @afoix.bsky.social and @denzibubs.bsky.social share their highlights from #CBIAS2025 @cbias.bsky.social, with all three emphasising the welcoming atmosphere. Check out the reasons that #CBIAS2026 should be in your calendar⤵️ focalplane.biologists.com/2026/01/12/c...
focalplane.biologists.com
Crick BioImage Analysis Symposium (2025) - a review - FocalPlane
Crick BioImage Analysis Symposium (2025) - a review - News
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Royal Microscopical Society @royalmicrosoc.bsky.social · 05/01/2026
Applications for our Section Awards are now *OPEN*😃 These awards are chosen by each of our Scientific Committees, in recognition of outstanding scientific achievements across all forms of microscopy, imaging and flow cytometry. Find out more and apply by 28 February: ow.ly/1gap50XRV7j
Two colleagues standing indoors, one presenting an award plaque and a glass trophy to the other against a wooden panel background.
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Stefania Marcotti @lankylaste.bsky.social · 02/01/2026
✨New Year's resolutions involve learning something new?✨ Then apply for our “Introduction to Image Analysis” workshop in Cardiff in May 2026! Deadline for applications is January 16th. 🔗⬇️ www.rms.org.uk/rms-event-ca... @royalmicrosoc.bsky.social @david-j-barry.bsky.social @martinjones.bsky.social
rms.org.uk
Introduction to Image Analysis 2026
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