Want to enhance your image analysis skills with napari? We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data. 🕒 Applications close on 15 September. Learn more and apply 👇 www.crick.ac.uk/whats-on/cbi...

🔥🔥🔥 Upcoming plugin for BoneJ+, Anisotropy+ running on Intel, NVIDIA and AMD GPUs at the same time! This one uses fields of line probes to determine the fabric tensor and calculate the degree of anisotropy, a measure of underlying texture orientation and scale. Looking good for release next week 🤞

(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

✍ If you're having difficulty writing #BioimageAnalysis code that enables others to follow your workflow, have a look at @haesleinhuepf.bsky.socials slides on „Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI“ from the #EMBOlsm25. To the slides: 👉 doi.org/10.5281/zeno...

Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇

GloBIAS conference Kobe 2025, the registration for the symposium is still open, until Sept 15th! bit.ly/GloBIAS2025-...

we have been working on this for some years and finally out!

Some rough edges, but it works! #Fiji MCP server (+ Claude desktop) can do things in Fiji (get some info about the current state of the app, execute groovy scripts...).

First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social - "This will be a long week, but it will change your life". iac.hms.harvard.edu/bobiac/2025/

We built StarDist to detect cells in volumetric microscopy and jointly infer closed curved parametric surfaces for each cell. It's an example of an interpretable machine learning approach. More detail in the blog post and preprint. www.focolab.org/post/surfdis...

Are you developing with TrackMate? If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration. Details on the forum: forum.image.sc/t/upcoming-b...

Using #QuPath with HISTAI SPIDER Colorectal Module Repository github.com/sbalci/spide... Video www.youtube.com/watch?v=8tLO... #pathsky #digitalpathology #pathology #pathologist

✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later. @napari.org#eLife

@kbias.bsky.social, @pmsampaio.bsky.social, @tischi.bsky.social, Rocco D'Antuono, ‪and @haesleinhuepf.bsky.social ‬ did a great job of pulling the data together, to describe who we are, where we want to get, and how we get there together. Check out the preprint and join us today! (5/5)

‪It has been lovely to meet Kota @kbias.bsky.social after all these years! #imageanalysis @eurobioimaging.bsky.social

The application deadline for our next round of 🔬Training Grants is this Friday 6 June. www.biologists.com/grants/jcs-f...

When it comes to creating plots of your data, are you team 'web apps' or 'vibe coding' with genAI-based tools? 📊 In this post, Joachim Goedhart @joachimgoedhart.bsky.social‬ discusses the potentials and pitfalls of both approaches in data visualization:

I do agree. Well done!

Imaging 4 All - @globalbioimaging.bsky.social have launched their 2nd call for applications. Researchers from low- and middle-income countries can apply to receive support to visit imaging facilities & attend training courses. Deadline: 15 August 2025 focalplane.biologists.com/2025/05/20/i...

The #quarep-limi wg12 image & analysis publication workshop @ #ELMI2025 quite successful!

Image data & analysis publication check list team ( #quarep-limi wg12) getting ready for the workshop this afternoon #ELMI2025

Day 2 at #ELMI2025: participants and excibitors enjoying good coffee and conversations ☕🤝

#elmi2025 working toward joining forces of builders and creators to share *community tools* @eulimi.bsky.social @bioimagingna.bsky.social -> submit your tool (elmi.embl.org/tools/)

#ELMI2025 500 participations

Reminder: the @globias.bsky.social 2025 symposium is happening Oct 26-31 in Kobe, Japan, and, on top of many other cool bioimage analysis events, several members of the napari core team will be leading a napari hackathon. 🧑‍💻👩‍💻👨‍💻 Registration deadline is Jun 15! www.globias.org/activities/b...

So much looking forward to this! 🤩 We're thrilled to be running a new instance of our "Advanced Methods in Bioimage Analysis" course. It's going to be a blast! Apply by June 4th.

I posted an announcement about the GloBIAS2025 Kobe to the forum.image.sc. Added some more details, a lighter version of the conference website. #GloBIAS forum.image.sc/t/globias-co...

A great work: A part of my PhD study was confirmed. journals.plos.org/plosone/arti...

Just pushed v0.3.0 which builds in the lovely suite of LUTs created by @jamesdmanton.bsky.social also installable directly into FIJI at sites.imagej.net/JDM_LUTs/luts/

Turn images into insights! Join VIB's imaging workshops in Antwerp: 🔬🖥️ Fiji Image Processing (18/06): Build your first analysis pipeline 🔬🖥️ #QuPath Bioimage Analysis (19/06): Segment, classify & script your images For life scientists ready to level up. Details 👉 vibbio.tech/43sI2fp #bioimaging

The guru's talk... #GloBIAS

#GloBIAS conference 2025 Kobe, Deadline extended to June 15th! This includes the training school, two hackathons, and taggathon registration, not only the symposium (... but sorry, the travel grant for the training school has closed)

Next #GloBIAS seminar coming up. Curtis Rueden will present on 'Fiji with Python power'. To get the link please register here: www.globias.org/activities/b...

#HappyFluorescenceFriday! #microscopycommunity Join @bioimagingna.bsky.social Early Career WG for our Career Speaker Series on The BioImaging ToolBox: “Pre-nalysis”, Imaging, Analysis and Processing” next Thursday , May 1 Learn More & Register here buff.ly/BHGomlc

📢 Learn #QuPath across 🇵🇹! The 4th edition of our Intro to QuPath course is happening: 🗓️ May 21–23, 2025 📍 PPBI Nodes across Portugal 🔹 Register by May 11 📝 Info & registration: see comments

Want to hear more about the history of @cellprofiler.bsky.social , and about what comes next? Come listen to @gnodar.bsky.social and I talk about it tomorrow at the @globias.bsky.social seminar series - 5pm CEST/11am CDT/ 8 am PDT. Register NOW (so we have time to send you the link!) at link below!

Our next Atlantic community meeting is coming up! Wed 8:30am SFO / 11:30am NYC / 5:30pm Paris. Come chat about napari 0.6.0 (due imminently! 😅), ask for advice, demo your cool plugin! Agenda: hackmd.io/BXWDZ3i8Q6OA... Zoom: numfocus-org.zoom.us/j/8404893043... Calendar: napari.org/stable/commu...

👉🏼 Attention #LABICommunity Tomorrow, April 23, is the last day to apply for the free online Latin American CellProfiler Workshop! A great opportunity to dive into image analysis using CellProfiler. 🔗 broad.io/latam_workshop2025

New tool: OrgaMeas www.sciencedirect.com/science/arti...

If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2) forms.gle/C8dUpg8qZkbD... #bioimaging #microscopy #bioimageanalysis

The FIRST GloBIAS conference is happening in Kobe, Japan, and we launched the webpage and the registration form. Training school, Hackathon, Taggathon, and Symposium with talks, posters, open-source software lounge, call-4-help on stage! #BioimageAnalysis #GloBIAS

In the past 2 days, we had the great pleasure to host an in-person workshop at @istaresearch.bsky.social with the collaboration of @globias.bsky.social, @carpentries.carpentries.org and @istaustria-iof.bsky.social. We wanted to create a go-to course for image analysis in Python. Info in the thread!

Featured image with Julia Peloggia de Castro Taken late at night by @jupeloggia.bsky.social, the image depicts a zebrafish embryo with active mitochondria labelled. Find out about Julia and the story behind the image from the Node-FocalPlane image competition: thenode.biologists.com/featured-ima...

Our latest preprint list is now up on FocalPlane! Our list this week focusses on research using microscopy tools to answer questions in biology. As always, please let us know if there are other preprints that you’d like to see included. focalplane.biologists.com/2025/04/04/m...

🎤 AI4Life continues its presence at the @bioimagearchive.bsky.social course! Esti presents BioImage.IO, emphasizing the importance of keeping AI models accessible, reproducible, and interoperable. With so many image analysis tools out there, common model standards are the way forward!

Great initiative from #LABICommunity in 🇪🇨! A new survey aims to gather detailed data to drive capacity-building initiatives at local level. If you work with microscopy or image analysis, you can complete it 🔗 shortlink.uk/YIuu Let’s strengthen bioimaging in LAC! 🌎

Now released a software used in our paper to analyze root growth from TrackMate data! You can analyze data of root tip nuclei easily via a simple GUI. Paper: https://academic.oup.com/pcp/article/64/11/1262/7323573 GitHub: https://github.com/TakaakiYonekura/RootDataAnalysis

At the @training.ebi.embl.org course on Microscopy Data Analysis: Machine Learning & @bioimagearchive.bsky.social, Dominik Kutra from @ilastik-team.bsky.social introduced ilastik and how it supports image analysis. Now, it's time for a hands-on session! 🚀 #BioImageAnalysis #MachineLearning

Exploring the Uncharted Waters of Endothelial Tip Cell Migration: A Story of Aquaporins, Hydrostatic Pressure, and Angiogenesis 💧🩸 Here, Li-Kun Phng @phnglab.bsky.social tells the 'behind the paper' story that includes twists and turns, and a revisit of an observation made more than 10 years ago: