Want to learn about the latest trends and developments in bioimage analysis? Join us for the GLOBIAS workshop in Dortmund this November! I will be hosting a session on foundation models / AI. www.globias.org/activities/g...

GloBIAS2026 Workshop Dortmund

GloBIAS 2026 Bioimage Analysts' Workshop Registration is open! Register with this link! 10-13 November, 2026 - Tuesday to Friday Leibniz-Institut für Analytische Wissenschaften – ISAS – e. V. (https...

globias.org

I taught my first @carpentries.carpentries.org workshop. Yes it was a private non-official one to some colleagues but still a worthwhile and rich experience. I wrote more details on my last blog post! marcodallavecchia.gitlab.io/web/blog/tea...

Additionally, for the love of God stop generating random AI images for silly attention-catching posts. It's not even pretty and it most often has the opposite effect of drawing people away

Erick Ratamero@erickratamero.com · 4mo ago

Recently, every time I need an image to illustrate something on one of my slides, I go to Wikimedia Commons and get something with a license and a clear attribution. It never takes more than 2 minutes and it does not use the water supply of a small town. Your lazy AI art is not even saving time.

apparently Wikipedia has more rigorous standards than every university on the planet, university administrators, edtech enthusiasts, (certainly more than) AI bros, several prominent academic journals, and too many professors and teachers

Emanuel Maiberg@emanuelmaiberg.bsky.social · 4mo ago

after much deliberation and giving AI the benefit of the doubt, Wikipedia editors have had enough of AI slop. New policy bans LLM generated content, periodt www.404media.co/wikipedia-ba...

Loving the plan!

BrainGlobe@brainglobe.info · 5mo ago

BrainGlobe has a new roadmap! Somewhat overdue, the March 2026 roadmap summarises our recent progress, and our priorities for the coming year. Read more: brainglobe.info/community/ro...

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/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

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API

Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

github.com

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io

An Introduction to OME-Zarr for Big Bioimaging Data

ome-zarr-book.readthedocs.io

Next blog post! I built another simple Marimo app to explore FPs spectra and other properties. It was a fun little trip, I hope you find it insightful. Find it here: marcodallavecchia.gitlab.io/web/blog/mar...

🌟Join our Scientific Ambassador, Magdalena Schindler, on a scientific tour of her hometown! Meet the people and explore the facilities that make up the Node, and support Vienna's rich & collaborative imaging landscape. 🏛️🔬 📽️ Watch the video ⤵️ youtu.be/mCZmL8KF4fA

New blog post! Last year, I wrote some data visualization tips and pitfalls for a workshop, and I now ported it over to a @quarto.org manuscript with references and source code for the figures. Check it out here! marcodallavecchia.gitlab.io/web/blog/dos...

🏆Announcing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025! 🎉 Join us in celebrating the laureates at the award ceremony, featuring a special lecture from International Prize laureate representative from the BrainGlobe initiative. #OpenScience #Neuroscience

The Neuro – Irv and Helga Cooper Foundation Open Science Prizes: Meet the winners of an exceptional edition

This year’s edition of the Irv and Helga Cooper Foundation Open Science Prizes at The Neuro, organised by the Tanenbaum Open Science Institute, was exceptional in every way. With a record number of ap...

mcgill.ca

I'm happy to release into the wild my new professional and personal website marcodallavecchia.gitlab.io/web/ I finally found some time to reorganize ideas and redo the framework with @quarto.org You can read my first blog post on the website here! marcodallavecchia.gitlab.io/web/blog/web...

In preparation for our annual microscopy course I used #NotebookLM to gather resources about light-sheet microscopy and get ideas for teaching and get a better understanding. Then I listened to the audio summary, and I got mad at how decently good it was! notebooklm.google.com/notebook/3b5...

New guest blog by @marcodv.bsky.social about our open software summer school, held at @sainsburywellcome.bsky.social. neuroinformatics.dev/blog/perspec... Stay tuned for information about next years event, which will be bigger and better!

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

First day of work back in @istaustria-iof.bsky.social after 2 weeks exchange with the guys at @neuroinformatics.dev. Still processing all the ideas and new information in my brain, I hope to be able to write them down and make something concrete out of all of it very soon!

Marco Dalla Vecchia@marcodv.bsky.social · 12mo ago

What an experience, great people, great material and great environment. Thanks for making this possible and I hope this becomes a well established yearly tradition @neuroinformatics.dev

What an experience, great people, great material and great environment. Thanks for making this possible and I hope this becomes a well established yearly tradition @neuroinformatics.dev

SWC/GCNU Neuroinformatics Unit@neuroinformatics.dev · 12mo ago

Thank you to everyone who came to Open Software Week. We had a great time, and we hope you all left with new knowledge, ideas or collaborations. #niu_osw

Day 4 open software week #OSW by @neuroinformatics.dev, Hackday! It was really a cool experience to see people from different backgrounds coming together and try things, learn with each other and contributing to open source resources Thanks a lot to the instructors for guiding and supporting us!

Day 4 of the open software week #OSW, all about big jmaging data and @zarr.dev @openmicroscopy.org One of my favorite days so far, lots of discussions with mang experts in the field from very different backgrounds. I understood Zarr much better and we got to write blog posts on selected topics!

Day 3 of open software week #OSW by @neuroinformatics.dev! Super cool demos and time to dig deep into 2D and 3D visualizations of the mapped atlas with cells, segmented structures, and annotations. You can even make movies or html exports! Looking forward to the big data track next!

SWC/GCNU Neuroinformatics Unit@neuroinformatics.dev · 12mo ago

The third day of Open Software Week is underway. On the @brainglobe.info track, students are learning how to use the BrainGlobe Python ecosystem to write their own scripts. Starting with creating visualisations using brainglobe-heatmap: brainglobe.info/documentatio... #niu_osw

Day 2, open software week #OSW by @neuroinformatics.dev Today was all about @brainglobe.info and a little sneaky visit of the imaging facility 🔬 Most of the material below was at-your-own-pace tutorials, but the in-house expertise is unparalleled making discussions rewarding and stimulating!

SWC/GCNU Neuroinformatics Unit@neuroinformatics.dev · 12mo ago

The BrainGlobe track started with an introduction to image analysis with @napari.org, and then tutorials on how to use @brainglobe.info to register data to atlases, and how to detect cells in whole-brain microscopy images. All our tutorials are online: brainglobe.info/tutorials #niu_osw

Day 1 of Open Software Week #OSW organized by @neuroinformatics.dev! Really impressed with everything I've seen so far. Great lecture material, great team synergies and great organization. Wanna peak at the material? Take a look here: neuroinformatics.dev/open-softwar... Looking forward to Day 2!

I'm headed to London where in the next two weeks I'll learn from the amazing people at @neuroinformatics.dev! I'm super excited for the open software week #OSW to learn all about large image data handling, @brainglobe.info and much more!

Please engage with our announcement about curriculum development for Carpentries workshops about genAI. 🗣️ If you have experience, expertise, and perspectives to share in a nuanced discussion on this topic, please join the upcoming sessions on 12th August. Details: carpentries.org/blog/2025/08...

AI Carpentry? Helping learners make better choices with genAI.

In two recent community discussion sessions, we explored what mental model of machine learning/deep learning we could teach to learners already familiar with the basics of programming, to help them sa...

carpentries.org

@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)

GloBIAS: strengthening the foundations of BioImage Analysis

There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...

arxiv.org

We've been trying nnInteractive (github.com/MIC-DKFZ/nap...) to quickly create labeled data for later training an Omnipose model. I whatever black magic you did there, keep at it! It's such a life-changer!

Any scikit-image fans in Vienna? The skimage team would like to meet in Vienna for a code sprint Aug 14-16 ahead of EuroSciPy. We'd super appreciate it if someone's workplace can host us! All we need is electricity, natural light, and (most important) walking distance to coffee. ☕️😂🙏

If a community of software developers struggles with version control of their own documents, I don't think I have a chance 👀 look at that file name 😅

napari@napari.org · last yr.

Hello all, Hopefully the last community meeting now before 0.6.0 lands 😅 This has been a lot of hard work the last weeks by multiple people! Want to discuss the release or have any napari questions for core devs or want to show a cool demo? Come join tomorrow! Details below