iiinova — where your digital self keeps evolving

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

1104

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.

040

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

01213

Marco Dalla Vecchia @marcodv.bsky.social · 08/08/2026

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

000

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...

01510

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

040

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

061

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

101090324

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...

88444

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

16224

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

23016

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

021

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

042

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

062

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...

0104

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

172

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

031

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.

095

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

14032

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!

041

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

031

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!

030

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!

150

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!

051

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!

030

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 Centre

140

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

071

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...

022

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!

1114

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. ☕️😂🙏

298

Marco Dalla Vecchia @marcodv.bsky.social · 15/04/2025

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 😅

140

Marco Dalla Vecchia @marcodv.bsky.social · 09/04/2025

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!

GloBIAS and Data Carpentry members group picture

12510

Reposted by Marco Dalla Vecchia

Gabriel Krens @gkrens.bsky.social · 07/04/2025

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

1124

Reposted by Marco Dalla Vecchia

the Node @the-node.bsky.social · 27/03/2025

🎉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

"Cell-estial bloom" Image from Özge Özgüç:
A ‘Cell-estial bloom’ of human induced pluripotent stem cells (hiPSCs) flourishes on a micropatterned island. This image presents a colony of live hiPSCs, with fluorescently labelled Lamin B delineating the nuclear lamina within each cell. Acquired with a Zeiss LSM 880 Airyscan microscope, this maximum intensity projection is enhanced with depth-coded coloring to reveal the captivating three-dimensional landscape.

"Dancing actinotroch" by Allan Carrillo-Baltodano:
Actinotroch larva of a phoronid worm with phalloidin shown in yellow and acetylated tubulin in magenta. Imaged with a Zeiss LSM 800 at 10 x magnification.

"Who’s active?" by Julia Peloggia de Castro:
The image depicts a zebrafish embryo at 9 hours post-fertilisation on a lateral view. Cells are stained with MitoTracker, which labels active mitochondria, and cell membranes are labelled in cyan with a EGFP transgenic membrane tag. Image was taken using a 20x objective on a spinning disk confocal microscope.

59728

Marco Dalla Vecchia @marcodv.bsky.social · 26/03/2025

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! 😂

Overlay of good FF image with homogeneity and centrality scores

Overlay of a wrong cat picture instead of an FF image

010

Marco Dalla Vecchia @marcodv.bsky.social · 07/03/2025

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

color-coded z projection of a weevil head acquired at Zeiss light-sheet 7 microscope

0182

Reposted by Marco Dalla Vecchia

Damian Dalle Nogare @damiandn.bsky.social · 01/03/2025

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-...

forum.image.sc

Fiji 2024 Year in Review: Milestones and Roadmap

Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...

1234

Reposted by Marco Dalla Vecchia

GloBIAS @globias.bsky.social · 03/02/2025

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

tinyurl.com

Update the Data Carpentries Bioimage Analysis with Python Curriculum

Data Carpentries BioImage Analysis - update with a Python Curriculum Join us to update the Data Carpentries Bioimage Analysis Curriculum with a Python Curriculum! We’re inviting bioimage analysis prof...

11512

Reposted by Marco Dalla Vecchia

Nathan Yau @flowingdata.com · 13/02/2025

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...

flowingdata.com

Defense Against Dishonest Charts

This is a guide to protect ourselves and to preserve what is good about turning data into visual things.

32501250

Marco Dalla Vecchia @marcodv.bsky.social · 03/02/2025

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

012

Marco Dalla Vecchia @marcodv.bsky.social · 28/01/2025

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?

000

Marco Dalla Vecchia @marcodv.bsky.social · 24/01/2025

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!

130

Reposted by Marco Dalla Vecchia

GloBIAS @globias.bsky.social · 13/01/2025

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...

forms.gle

02522

Marco Dalla Vecchia @marcodv.bsky.social · 16/01/2025

Come and join our growing image analysis team at ISTA!

000

Marco Dalla Vecchia @marcodv.bsky.social · 29/11/2024

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

030

Marco Dalla Vecchia @marcodv.bsky.social · 21/11/2024

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...

0114