Marco Dalla Vecchia
@marcodv.bsky.social
Microscopy and Image Analyst Expert at ISTA
https://marcodallavecchia.gitlab.io/web
https://marcodallavecchia.gitlab.io/web
Reposted by Marco Dalla Vecchia
Today I'm announcing a new digital textbook ππ₯οΈ, "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
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Today I'm announcing a new digital textbook ππ₯οΈ, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
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...
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...
Exploring Fluorescent Proteins with Marimo β marcodallavecchia/web
Access, explore and interact with FP properties
marcodallavecchia.gitlab.io
October 20, 2025 at 6:17 AM
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...
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...
Reposted by Marco Dalla Vecchia
πJoin 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. ποΈπ¬
π½οΈ Watch the video ‡οΈ
youtu.be/mCZmL8KF4fA
Meet the people and explore the facilities that make up the Node, and support Vienna's rich & collaborative imaging landscape. ποΈπ¬
π½οΈ Watch the video ‡οΈ
youtu.be/mCZmL8KF4fA
October 14, 2025 at 1:31 PM
πJoin 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. ποΈπ¬
π½οΈ Watch the video ‡οΈ
youtu.be/mCZmL8KF4fA
Meet the people and explore the facilities that make up the Node, and support Vienna's rich & collaborative imaging landscape. ποΈπ¬
π½οΈ Watch the video ‡οΈ
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...
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...
Dos and Donβts of data visualization β marcodallavecchia/web
A few sample cases to understand the importance of proper data visualization
marcodallavecchia.gitlab.io
October 10, 2025 at 6:59 AM
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...
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...
Reposted by Marco Dalla Vecchia
πAnnouncing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025!
π 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
π 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
The Neuro β Irv and Helga Cooper Foundation Open Science Prizes: Meet the winners of an exceptional edition
This yearβs 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...
www.mcgill.ca
October 8, 2025 at 7:29 PM
πAnnouncing the laureates of the Neuro - Irv and Helga Cooper Foundation Open Science Prizes 2025!
π 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
π 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!
October 7, 2025 at 10:58 AM
Thanks a lot! I find it extremely helpful to make this little interactive apps to better understanding or showcasing concepts. Glad you liked it!
It works relatively well with the extension! github.com/marimo-team/...
GitHub - marimo-team/quarto-marimo: marimo extension for Quarto β‘ run reactive code inside Quarto
marimo extension for Quarto β‘ run reactive code inside Quarto - marimo-team/quarto-marimo
github.com
October 6, 2025 at 9:26 PM
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...
Image Affine Transformation Demo β marcodallavecchia/web
Live demo of image affine transformations, powered by Marimo.
marcodallavecchia.gitlab.io
October 6, 2025 at 6:28 AM
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 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 β marcodallavecchia/web
my corner of the web
marcodallavecchia.gitlab.io
October 6, 2025 at 6:26 AM
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 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
October 1, 2025 at 2:39 PM
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...
notebooklm.google.com/notebook/3b5...
Sign in - Google Accounts
notebooklm.google.com
September 20, 2025 at 11:20 AM
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/notebook/3b5...
Love the marimo app for this use case! Takes a while to load, but super smooth after that.
September 18, 2025 at 7:12 AM
Love the marimo app for this use case! Takes a while to load, but super smooth after that.
Reposted by Marco Dalla Vecchia
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!
neuroinformatics.dev/blog/perspec...
Stay tuned for information about next years event, which will be bigger and better!
September 12, 2025 at 9:36 AM
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!
neuroinformatics.dev/blog/perspec...
Stay tuned for information about next years event, which will be bigger and better!
Reposted by Marco Dalla Vecchia
We're happy to announce the 2025 International OME-NGFF workshop π
π Dates:
- Symposium: Nov 10β11, 2025
- Hackathon: Nov 12β14, 2025
π Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...Β
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x π§΅)
π Dates:
- Symposium: Nov 10β11, 2025
- Hackathon: Nov 12β14, 2025
π Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...Β
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x π§΅)
August 25, 2025 at 9:07 AM
We're happy to announce the 2025 International OME-NGFF workshop π
π Dates:
- Symposium: Nov 10β11, 2025
- Hackathon: Nov 12β14, 2025
π Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...Β
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x π§΅)
π Dates:
- Symposium: Nov 10β11, 2025
- Hackathon: Nov 12β14, 2025
π Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...Β
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x π§΅)
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
August 27, 2025 at 12:33 PM
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
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
#niu_osw
August 25, 2025 at 6:13 AM
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
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
#niu_osw
August 16, 2025 at 8:25 AM
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!
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!
August 16, 2025 at 8:09 AM
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!
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
Thanks a lot @neuroinformatics.dev for organizing this
August 15, 2025 at 7:09 AM
Excited to see if some of the blog posts actually end up being officially published!
Thanks a lot @neuroinformatics.dev for organizing this
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!
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!
August 15, 2025 at 7:07 AM
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!
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!
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!
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
Starting with creating visualisations using brainglobe-heatmap:
brainglobe.info/documentatio...
#niu_osw
August 14, 2025 at 7:45 AM
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!
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 π¬
Most of the material below was at-your-own-pace tutorials, but the in-house expertise is unparalleled making discussions rewarding and stimulating!
Today was all about @brainglobe.info and a little sneaky visit of the imaging facility π¬
Most of the material below was at-your-own-pace tutorials, but the in-house expertise is unparalleled making discussions rewarding and stimulating!
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
All our tutorials are online: brainglobe.info/tutorials
#niu_osw
August 12, 2025 at 5:59 PM
Day 2, open software week #OSW by @neuroinformatics.dev
Today was all about @brainglobe.info and a little sneaky visit of the imaging facility π¬
Most of the material below was at-your-own-pace tutorials, but the in-house expertise is unparalleled making discussions rewarding and stimulating!
Today was all about @brainglobe.info and a little sneaky visit of the imaging facility π¬
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.
Materials, documentation, scientific discussion, communication channels and more: everything is open access, open for discussion and open to contribute.
August 11, 2025 at 8:11 PM
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.
Materials, documentation, scientific discussion, communication channels and more: everything is open access, open for discussion and open to contribute.
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!
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!
August 11, 2025 at 8:08 PM
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!
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!
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!
I'm super excited for the open software week #OSW to learn all about large image data handling, @brainglobe.info and much more!
August 10, 2025 at 7:20 AM
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!
I'm super excited for the open software week #OSW to learn all about large image data handling, @brainglobe.info and much more!