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...

🏆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

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!

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!

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!

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...

@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)

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 😅

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!

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

Very happy to have the @globias.bsky.social & @carpentries.carpentries.org workshop at @istaresearch.bsky.social with key contributions of @Tereza Belinova, @marcodv.bsky.social and @sommerinvienna.bsky.social from our @istaustria-iof.bsky.social faculty team

🎉Congratulations to the Top 3 images from the Node–FocalPlane image competition! 1️⃣"Cell-estial bloom" by @oozguc.bsky.social 2️⃣"Dancing actinotroch" by @allancarbal.bsky.social 3️⃣"Who’s active?" by @jupeloggia.bsky.social thenode.biologists.com/results-from... @focalplane.bsky.social #biologists100

As part of our regular health check of our systems at @istaustria-iof.bsky.social, we acquire and analyze flat-field images automatically through our internal database. Today I noticed a particularly strange FF image my script analyzed, but of course I am going to leave it there! 😂

Let's give it a go to my first #FluorescenceFriday Here's a color-coded Z-projection of a weevil head imaged on our Zeiss light-sheet 7 with pure green autofluorescence. Looking very cool, but also ominous! @istaustria-iof.bsky.social

Wow, this is big: "Fiji can now be launched in a Python-first mode, where first Python is started, then Fiji is started via the PyImageJ library. In this mode, Fiji is fully integrated with the active Python environment" forum.image.sc/t/fiji-2024-...

Bioimage analysis professionals: join us in-person for a workshop at ISTA in Klosterneuburg, Austria, April 7–8, 2025. A workshop to adapt and expand the current Data Carpentries image processing curriculum. Information & registration: tinyurl.com/3twkax2k

Dishonest charts are coming from all directions, and they're only going to hit harder. Unless we push back. So, an interactive guide: Defense Against Dishonest Charts flowingdata.com/projects/dis...

Join us in person for shaping the future of this already great curriculum! #globias #image-analysis #microscopy

I would love to get more into using Marimo notebooks (docs.marimo.io) but I struggle to find a good image visualization approach. Napari doesn't seem to work, and ipywidgets neither. My current solution is to use plotly with marimo.ui elements, but it's not very efficient. Anyone has alternatives?

I often struggled to track objects in movies in Python. As much as I love [Btrack](btrack.readthedocs.io), it is sometime difficult to make sense of the configuration params. I recently found [LapTrack](github.com/yfukai/laptr...), a simple TrackMate-inspired tracker working with one param!

Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler. 💡 Details: www.globias.org/activities/c... 🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...

Come and join our growing image analysis team at ISTA!

Don't you hate it when the last time you modified your Jupyter notebook was *next year*? 😂

I think I'm getting addicted to new #BigTrace in #Fiji by @ekatrukha.bsky.social 😅 So satisfying! Here's a live demo as I segment an entire notochord using the 'one-click' tracking tool and instantly straighten the entire thing for later analysis! Try it out here: github.com/ekatrukha/Bi...