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

Absolutely brilliant.
I mean if it can run inside an SVG image bsky.app/profile/psy-...

You're joking right?

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

Loving the plan!

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

image.coop/blog/posts/2...

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

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

An Introduction to OME-Zarr for Big Bioimaging Data

Today I'm announcing a new digital textbook 📖🖥️, "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...

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...

🏆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

Thanks a lot! I find it extremely helpful to make this little interactive apps to better understanding or showcasing concepts. Glad you liked it!

GitHub - marimo-team/quarto-marimo: marimo extension for Quarto ⚡ run reactive code inside Quarto marimo extension for Quarto ⚡ run reactive code inside Quarto - marimo-team/quarto-marimo

It works relatively well with the extension! github.com/marimo-team/...

For those interested in interactive apps and affine transform, I already included another post on understanding the affine transform matrix for images here marcodallavecchia.gitlab.io/web/blog/ima...

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...

I think most people are going towards Xarray and what is built ontop of it such as spatial-image and lazyslide

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...

Love the marimo app for this use case! Takes a while to load, but super smooth after that.

Some of the summer school participants, gathered after the summer school hackday.

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!

Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland

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 🧵)

Cool! Is this anyhow related to the types of projections done here: bigwww.epfl.ch/demo/edf/?

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!

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

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!

Excited to see if some of the blog posts actually end up being officially published!

Thanks a lot @neuroinformatics.dev for organizing this

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!

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!

More than anything, I was quite impressed about the #open-source philosophy at the core of everything for the event and the whole team.

Materials, documentation, scientific discussion, communication channels and more: everything is open access, open for discussion and open to contribute.