Marco Dalla Vecchia

🌟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.

Entrance door to the Sainsbury Wellcome Centre

Lecture hall of welcome slides

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!

Image of the airport gate display showing London destination

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!

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...

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...

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...

@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 had a case in the past in which segmentation on brightfield images was near impossible and having fluorescence made it straightforward. We then had another user coming with brightfield only data, and being able to predict fluorescence signal from this new data for segmentation would have saved us

From the screenshot, these spots are extremely well defined and easy to detect with any DoG or LoG methods. I would do this in Fiji but you could give it a try to SpotMAX

In our user base, we experienced several times corrupted files for no apparent reasons. We tried to boil it down to machine, data storage location, loss of connection but nothing seems to relate. A curiosity which Jmaris version are you working with? Most of our corruptions happened with v9

Very cool :)

Napari 3D view screenshot depicting a labeled bacteria dataset

And here's the full labeling by one of our users for the full training patch. Some errors to still correct, but such a time saver!