Marco Dalla Vecchia

Had fun preparing a more interactive version of our usual slides for our hands-on demo session on the light-sheet! It's definitely 'in-development' still, but it's interactive through Marimo WebAssembly, give it a little time to load and try it! iof-group.gitlabpages.ista.ac.at/teaching/lig...

We have a position open in our core facility in the @pasteur.fr . Please share it and / or apply! forum.image.sc/t/research-e...

OME-Zarr 0.6 allows to compose multi-modal image data across dimensionalities into a joint dataset and ingest it into a supporting viewer of your choice. Combining image data across scales from µm 🧫 to cm 🧠 and beyond will be much easier now! Dataset source: rodare.hzdr.de/record/3131

I was never a person to look at "numbers going up", but I admit it feels good to see my (and our team's) increase in usage of our institute GitLab instance for project and infrastructure.

Interested in image analysis and a service role in a dynamic and growing facility? Come and joy our image analysis team! Feel free to reach out for any questions or doubts. ista.ac.at/en/job/?titl...

Live in: 🇦🇹 Born in: 🇮🇹 Parents: 🇮🇹 Grandparents: 🇮🇹 Been to: 🇵🇹 🇪🇸 🇫🇷 🇲🇨 🇱🇺 🇩🇪 🇦🇹 🇨🇭 🇧🇪 🇳🇱 🇮🇹 🇩🇰 🇨🇿 🇭🇺 🇸🇮 🇸🇰 🇭🇷 🇪🇬 🇹🇳 🇹🇷 🇬🇷 🇬🇧 🇷🇴 🇨🇴 🇪🇨 🇨🇺 🇺🇸 🇲🇽 🇵🇰

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...

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

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...

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

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

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 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!

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)

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 😅

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! 😂