π£Weβre back π¬ππ₯οΈ!
#CBIAS2026 returns 23β24 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
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
π
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
Hi Thorsten, great to hear from you, and how unfair your situation now is... Just to let you know some good news: I recently benchmarked your ridge detection plugin and found it quite robust (the best...) in measuring length. Take care!
fke mail
Warning: another round of fake Kota sending emails to you! Be careful, if the mail address contains "president", it's not from me.
ππ° 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 RΟiv-Maker
@henriqueslab.bsky.social
rxiv-maker.henriqueslab.org
Paper: arxiv.org/html/2508.00...
Anthony A. Hyman will become EMBLβs 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.
Four men opening sake barrel in a ceremonial way
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?
Weβre running a two-day training event on how to use napari to effectively analyse your bioimaging data.
π Applications close on 15 September.
Learn more and apply π
www.crick.ac.uk/whats-on/cbi...
π₯π₯π₯ 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 π€
(1/14) Iβm happy and proud to introduce: SpinePy β 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 yourselfπ§΅(1/9)
www.nature.com/articles/s41...
β If you're having difficulty writing #BioimageAnalysis code that enables others to follow your workflow, have a look at @haesleinhuepf.bsky.socials slides on βReproducible Bio-Image Analysis using Python, Napari, Jupyter and AIβ from the #EMBOlsm25.
To the slides: π 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). π
Especially, you can still submit your bioimage analysis question and get your feedback from 140 researchers, many of whom are world-leading experts at call4help session see: call4help.let-your-data-speak.com
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...
