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Marco Dalla Vecchia

@marcodv.bsky.social
437 followers 603 following 59 posts

Microscopy and Image Analyst Expert at ISTA marcodallavecchia.gitlab.io/web

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Reposted by Marco Dalla Vecchia
Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026
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
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Marco Dalla Vecchia @marcodv.bsky.social · 17/09/2026
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.
screenshot of GitLab activity heatmap
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Marco Dalla Vecchia @marcodv.bsky.social · 28/08/2026
I'm one day too late then!
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Marco Dalla Vecchia @marcodv.bsky.social · 28/08/2026
How come I didn't know about this?!
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Marco Dalla Vecchia @marcodv.bsky.social · 27/08/2026
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...
ista.ac.at
Job details
Job details
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Marco Dalla Vecchia @marcodv.bsky.social · 08/08/2026
Live in: 🇦🇹 Born in: 🇮🇹 Parents: 🇮🇹 Grandparents: 🇮🇹 Been to: 🇵🇹 🇪🇸 🇫🇷 🇲🇨 🇱🇺 🇩🇪 🇦🇹 🇨🇭 🇧🇪 🇳🇱 🇮🇹 🇩🇰 🇨🇿 🇭🇺 🇸🇮 🇸🇰 🇭🇷 🇪🇬 🇹🇳 🇹🇷 🇬🇷 🇬🇧 🇷🇴 🇨🇴 🇪🇨 🇨🇺 🇺🇸 🇲🇽 🇵🇰
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Reposted by Marco Dalla Vecchia
Constantin Pape @cppape.bsky.social · 30/06/2026
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...
globias.org
GloBIAS2026 Workshop Dortmund
GloBIAS 2026 Bioimage Analysts' Workshop Registration is open! Register with this link! 10-13 November, 2026 - Tuesday to Friday Leibniz-Institut für Analytische Wissenschaften – ISAS – e. V. (https...
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Marco Dalla Vecchia @marcodv.bsky.social · 30/04/2026
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...
marcodallavecchia.gitlab.io
I taught a full Carpentries workshop! – marcodallavecchia/web
My feedback and experience teaching the Building Better Research Software curriculum
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Marco Dalla Vecchia @marcodv.bsky.social · 08/04/2026
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
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Marco Dalla Vecchia @marcodv.bsky.social · 02/04/2026
Absolutely brilliant. I mean if it can run inside an SVG image bsky.app/profile/psy-...
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Marco Dalla Vecchia @marcodv.bsky.social · 02/04/2026
You're joking right?
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Reposted by Marco Dalla Vecchia
Aparna Nair @disabilitystor1.bsky.social · 27/03/2026
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
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Marco Dalla Vecchia @marcodv.bsky.social · 17/03/2026
Loving the plan!
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Reposted by Marco Dalla Vecchia
Image Cooperative @image.coop · 16/03/2026
Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
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Reposted by Marco Dalla Vecchia
Talley Lambert @talley.codes · 16/02/2026
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
github.com
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
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Reposted by Marco Dalla Vecchia
David Stansby @dstansby.bsky.social · 04/11/2025
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
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Marco Dalla Vecchia @marcodv.bsky.social · 20/10/2025
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...
marcodallavecchia.gitlab.io
Exploring Fluorescent Proteins with Marimo – marcodallavecchia/web
Access, explore and interact with FP properties
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Reposted by Marco Dalla Vecchia
eurobioimaging.bsky.social @eurobioimaging.bsky.social · 14/10/2025
🌟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
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Marco Dalla Vecchia @marcodv.bsky.social · 10/10/2025
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...
marcodallavecchia.gitlab.io
Dos and Don’ts of data visualization – marcodallavecchia/web
A few sample cases to understand the importance of proper data visualization
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Reposted by Marco Dalla Vecchia
Le Neuro (Institut-Hôpital neurologique de Montréal) @theneuro.bsky.social · 08/10/2025
🏆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
mcgill.ca
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...
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Marco Dalla Vecchia @marcodv.bsky.social · 07/10/2025
Thanks a lot! I find it extremely helpful to make this little interactive apps to better understanding or showcasing concepts. Glad you liked it!
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Marco Dalla Vecchia @marcodv.bsky.social · 06/10/2025
It works relatively well with the extension! github.com/marimo-team/...
github.com
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
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Marco Dalla Vecchia @marcodv.bsky.social · 06/10/2025
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...
marcodallavecchia.gitlab.io
Image Affine Transformation Demo – marcodallavecchia/web
Live demo of image affine transformations, powered by Marimo.
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Marco Dalla Vecchia @marcodv.bsky.social · 06/10/2025
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...
marcodallavecchia.gitlab.io
Personal & Professional Website – marcodallavecchia/web
my corner of the web
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Marco Dalla Vecchia @marcodv.bsky.social · 01/10/2025
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 · 20/09/2025
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...
notebooklm.google.com
Sign in - Google Accounts
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Marco Dalla Vecchia @marcodv.bsky.social · 18/09/2025
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 · 12/09/2025
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 · 25/08/2025
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 · 27/08/2025
Cool! Is this anyhow related to the types of projections done here: bigwww.epfl.ch/demo/edf/?
bigwww.epfl.ch
BIG > Extended Depth of Field
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Marco Dalla Vecchia @marcodv.bsky.social · 25/08/2025
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!
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Marco Dalla Vecchia @marcodv.bsky.social · 16/08/2025
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
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Marco Dalla Vecchia @marcodv.bsky.social · 16/08/2025
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 · 15/08/2025
Excited to see if some of the blog posts actually end up being officially published! Thanks a lot @neuroinformatics.dev for organizing this
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Marco Dalla Vecchia @marcodv.bsky.social · 15/08/2025
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 · 14/08/2025
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!
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Marco Dalla Vecchia @marcodv.bsky.social · 12/08/2025
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!
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Marco Dalla Vecchia @marcodv.bsky.social · 11/08/2025
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 · 11/08/2025
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 CentreLecture hall of welcome slides
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Marco Dalla Vecchia @marcodv.bsky.social · 10/08/2025
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 · 06/08/2025
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...
carpentries.org
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...
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Reposted by Marco Dalla Vecchia
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 10/07/2025
@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)
arxiv.org
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...
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Marco Dalla Vecchia @marcodv.bsky.social · 25/06/2025
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 · 12/06/2025
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 · 12/06/2025
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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Marco Dalla Vecchia @marcodv.bsky.social · 20/05/2025
Very cool :)
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Marco Dalla Vecchia @marcodv.bsky.social · 16/05/2025
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!
Napari 3D view screenshot depicting a labeled bacteria dataset
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Marco Dalla Vecchia @marcodv.bsky.social · 16/05/2025
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!
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Reposted by Marco Dalla Vecchia
Juan Nunez-Iglesias @jni.codes · 15/05/2025
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. ☕️😂🙏
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Marco Dalla Vecchia @marcodv.bsky.social · 15/05/2025
We've already inquired unfortunately it's not so easy to accommodate completely external events..
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