Miguel A. Ibarra Arellano reporting the Hackthon@GloBIAS conference Kobe 2025: focalplane.biologists.com/2026/04/01/h...

Interesting discussion here: analyst-analyst variability of analysis results. forum.image.sc/t/does-imari...

Introducing the Anthropic Science Blog. Increasing the pace of scientific progress is a core part of Anthropic’s mission. The Science Blog will feature new research and stories of how scientists are using AI to accelerate their work. Read the intro:

📣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

Is this bad

One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇

In the #BigVolumeBrowser news, there is a new awesome video tutorial about it made by certified magician Johanna M. Dela Cruz. Check it out: www.youtube.com/watch?v=c0fr... (1/2)

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI

In September 2024, I was diagnosed with ALS. Today, I can no longer speak, I am confined to a wheelchair, and I can no longer move my arms. It's really shitty. I will write here soon about how I am coping with this and how I am trying to stay cheerful. #ALS

Warning: another round of fake Kota sending emails to you! Be careful, if the mail address contains "president", it's not from me.

🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint Preprint updated: arxiv.org/abs/2508.00836

To help you select the right assay for a given application, we critically assessed and compared in vitro/in vivo assays to measure cell migration. Read and use our paper here: www.nature.com/articles/s41... Contact me if you need a PDF of the paper.

I came across a new textbook on light microscopy authored by Jeremy Sanderson; it looks like the essence has been extracted from "Understanding Light Microscopy"? academic.oup.com/book/61662

Also, the PDF or our preprint was created with Rχiv-Maker @henriqueslab.bsky.social rxiv-maker.henriqueslab.org Paper: arxiv.org/html/2508.00...

Anthony A. Hyman will become EMBL’s next Director General. He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999. www.embl.org/news/people-...

New paper from the @rouxlab.bsky.social on Nature Communications! We study how membrane tension is spatially organized in cells. Using the mechanosensitive probe Flipper-TR to visualize tension across the plasma membrane of adherent cells and to dissect the conditions needed for a gradient to happen

BIOIMAGE ANALYSTS ASSEMBLE!!! #CBIAS2025

Looks like someone is misusing GloBIAS and its president name to approach people for money transfers. Please note - GloBIAS will always send proper payment requests and has no need for members and volunteers to transfer money on their behalf.

Opening of the networking dinner by traditional sake opening ceremony #GloBIAS2025 #BioimageAnalysis @kbias.bsky.social @globias.bsky.social

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...

✍ 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