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Marco Dalla Vecchia @marcodv.bsky.social · 1d

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

Marco Dalla Vecchia @marcodv.bsky.social · 2d

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

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

github.com

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Marco Dalla Vecchia @marcodv.bsky.social · 2d

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...

Image Affine Transformation Demo – marcodallavecchia/web

Live demo of image affine transformations, powered by Marimo.

marcodallavecchia.gitlab.io

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Marco Dalla Vecchia @marcodv.bsky.social · 2d

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...

Personal & Professional Website – marcodallavecchia/web

my corner of the web

marcodallavecchia.gitlab.io

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Marco Dalla Vecchia @marcodv.bsky.social · 7d

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

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Marco Dalla Vecchia @marcodv.bsky.social · 18d

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...

Sign in - Google Accounts

notebooklm.google.com

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Marco Dalla Vecchia @marcodv.bsky.social · 20d

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

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Reposted by Marco Dalla Vecchia

SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 26d

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!

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

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Reposted by Marco Dalla Vecchia

Joel Lüthi @joelluethi.bsky.social · Aug 25

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 🧵)

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

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 27

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

BIG > Extended Depth of Field

bigwww.epfl.ch

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 25

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 · Aug 16

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 · Aug 15

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

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 16

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 · Aug 15

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

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 16

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!

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 15

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

Thanks a lot @neuroinformatics.dev for organizing this

Marco Dalla Vecchia @marcodv.bsky.social · Aug 15

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!

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 14

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 · Aug 13

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

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 12

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 · Aug 12

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

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 11

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.

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 11

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!

Entrance door to the Sainsbury Wellcome Centre

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Marco Dalla Vecchia @marcodv.bsky.social · Aug 10

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!

Image of the airport gate display showing London destination

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Reposted by Marco Dalla Vecchia

The Carpentries @carpentries.carpentries.org · Aug 6

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

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Reposted by Marco Dalla Vecchia

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Jul 10

@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

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Marco Dalla Vecchia @marcodv.bsky.social · Jun 25

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

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Marco Dalla Vecchia @marcodv.bsky.social · Jun 12

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

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Marco Dalla Vecchia @marcodv.bsky.social · Jun 12

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

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