Marvin Albert
@m-albert.bsky.social
Image Analysis and Data Management at the Department of Biosystems Science and Engineering of ETH Zürich in Basel
Reposted by Marvin Albert
Paris 13eme now.
December 1, 2025 at 7:12 AM
Paris 13eme now.
Reposted by Marvin Albert
November 25, 2025 at 1:06 PM
TrackMate now integrates even more cutting-edge detection, segmentation and tracking methods and makes them fun and easy to use!
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 9:33 PM
TrackMate now integrates even more cutting-edge detection, segmentation and tracking methods and makes them fun and easy to use!
Reposted by Marvin Albert
MASSIVE thank you to everyone involved in this year's I2K meeting - 32 SUPER sessions from our volunteer presenters, and so many super-engaged participants.
HUGE shoutout to Aditi from @bioimagingna.bsky.social for being the organizational wizard!
See you in the recordings and at next year's!
HUGE shoutout to Aditi from @bioimagingna.bsky.social for being the organizational wizard!
See you in the recordings and at next year's!
November 20, 2025 at 5:32 PM
MASSIVE thank you to everyone involved in this year's I2K meeting - 32 SUPER sessions from our volunteer presenters, and so many super-engaged participants.
HUGE shoutout to Aditi from @bioimagingna.bsky.social for being the organizational wizard!
See you in the recordings and at next year's!
HUGE shoutout to Aditi from @bioimagingna.bsky.social for being the organizational wizard!
See you in the recordings and at next year's!
Reposted by Marvin Albert
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Python package managers: uv vs pixi?
When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I don’t hear much ab...
jacobtomlinson.dev
November 18, 2025 at 12:56 PM
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Reposted by Marvin Albert
Thrilled to have presented @globias.bsky.social at the @latambioimaging.bsky.social Meeting last week! 🇦🇷🔬
I really enjoyed sharing our mission in both a lightning talk and with a poster. It was fantastic to connect with so many passionate bioimaging scientists!
Let's keep building this community!
I really enjoyed sharing our mission in both a lightning talk and with a poster. It was fantastic to connect with so many passionate bioimaging scientists!
Let's keep building this community!
November 17, 2025 at 6:39 PM
Thrilled to have presented @globias.bsky.social at the @latambioimaging.bsky.social Meeting last week! 🇦🇷🔬
I really enjoyed sharing our mission in both a lightning talk and with a poster. It was fantastic to connect with so many passionate bioimaging scientists!
Let's keep building this community!
I really enjoyed sharing our mission in both a lightning talk and with a poster. It was fantastic to connect with so many passionate bioimaging scientists!
Let's keep building this community!
Reposted by Marvin Albert
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
research.pasteur.fr
November 15, 2025 at 9:22 AM
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Reposted by Marvin Albert
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
November 13, 2025 at 5:08 PM
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
Reposted by Marvin Albert
Do you want to learn more about 25+ bioimage analysis tools, 100% for free? Sign up to attend Halfway to I2K today! tinyurl.com/Halfway-to-I...
Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...
Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...
#HappyFluorescenceFriday #microscopycommunity
Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events!
Submit by Oct 31: buff.ly/lMhK4vz
Website: buff.ly/QP36RZB
Register for the workshops: buff.ly/8nNAI18
Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events!
Submit by Oct 31: buff.ly/lMhK4vz
Website: buff.ly/QP36RZB
Register for the workshops: buff.ly/8nNAI18
Airtable | Everyone's app platform
Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.
buff.ly
November 3, 2025 at 10:04 PM
Do you want to learn more about 25+ bioimage analysis tools, 100% for free? Sign up to attend Halfway to I2K today! tinyurl.com/Halfway-to-I...
Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...
Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...
Reposted by Marvin Albert
I just finished my @unileipzig.bsky.social #LunchLecture. Thanks everyone for the vivid discussion and Nicole Koburger for hosting us!
The slides are online #openaccess 🧑🏫🔓 zenodo.org/records/1742...
The slides are online #openaccess 🧑🏫🔓 zenodo.org/records/1742...
October 23, 2025 at 11:19 AM
I just finished my @unileipzig.bsky.social #LunchLecture. Thanks everyone for the vivid discussion and Nicole Koburger for hosting us!
The slides are online #openaccess 🧑🏫🔓 zenodo.org/records/1742...
The slides are online #openaccess 🧑🏫🔓 zenodo.org/records/1742...
Reposted by Marvin Albert
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 – 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...
Reposted by Marvin Albert
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Reposted by Marvin Albert
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
September 23, 2025 at 3:48 PM
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
Reposted by Marvin Albert
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)?
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Next #GloBIAS seminar is coming up: join us on 22nd of September, 4 pm CEST to hear from Jean-Yves Tinevez about: The scientific added value of a core-facility dedicated to Bioimage Analysis services. Want to register? -> www.globias.org/activities/b...
September 18, 2025 at 9:26 AM
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)?
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
Reposted by Marvin Albert
And we'll round off 2025 on November 26th at 4pm with guest presentations by Giliane Rochat about lightsheet processing for OME-Zarrs & Flurin Sturzenegger about the ZMB Fractal task collection. (5/6)
September 16, 2025 at 7:46 AM
And we'll round off 2025 on November 26th at 4pm with guest presentations by Giliane Rochat about lightsheet processing for OME-Zarrs & Flurin Sturzenegger about the ZMB Fractal task collection. (5/6)
Reposted by Marvin Albert
We'll start the season next week on September 24th at 4pm with a guest presentation by @csoneson.bsky.social & @silviabarbiero.bsky.social about the ez_zarr library (see github.com/fmicompbio/e...) (3/6)
GitHub - fmicompbio/ez_zarr: GIve easy, high-level access to ome-zarr fileset
GIve easy, high-level access to ome-zarr fileset. Contribute to fmicompbio/ez_zarr development by creating an account on GitHub.
github.com
September 16, 2025 at 7:46 AM
We'll start the season next week on September 24th at 4pm with a guest presentation by @csoneson.bsky.social & @silviabarbiero.bsky.social about the ez_zarr library (see github.com/fmicompbio/e...) (3/6)
Reposted by Marvin Albert
We'll have the second meeting on October 28th at 4pm with a guest presentation by @m-albert.bsky.social about multiview-stitcher (github.com/multiview-st...) & dask-image (image.dask.org/en/latest/) (4/6)
GitHub - multiview-stitcher/multiview-stitcher: A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D. - multiview-stitcher/multiview-stitcher
github.com
September 16, 2025 at 7:46 AM
We'll have the second meeting on October 28th at 4pm with a guest presentation by @m-albert.bsky.social about multiview-stitcher (github.com/multiview-st...) & dask-image (image.dask.org/en/latest/) (4/6)
Reposted by Marvin Albert
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
September 16, 2025 at 7:46 AM
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
Reposted by Marvin Albert
🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮
www.scilifelab.se/news/ready-t...
www.scilifelab.se/news/ready-t...
Ready to shape the future of AI in life science?
The next call for DDLS Fellows is opening soon, offering an outstanding opportunity for ambitious young researchers to establish their own internationally competitive research groups. This round has a...
www.scilifelab.se
September 12, 2025 at 1:46 PM
🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮
www.scilifelab.se/news/ready-t...
www.scilifelab.se/news/ready-t...
Reposted by Marvin Albert
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
September 10, 2025 at 12:50 PM
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
Reposted by Marvin Albert
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
www.nature.com
September 10, 2025 at 9:37 AM
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Marvin Albert
New short paper from our lab @currentbiology.bsky.social, in which we discover of a new mode of cell motility for choanoflagellates: flagellar gliding. www.cell.com/current-biol... - A 🧵
Flagellar gliding in choanoflagellates
Freire-Delgado and Brunet discover a new mode of cell motility in choanoflagellates,
the closest relatives of animals. Under mild confinement, choanoflagellate move over
surfaces without cell deformat...
www.cell.com
September 9, 2025 at 6:12 PM
New short paper from our lab @currentbiology.bsky.social, in which we discover of a new mode of cell motility for choanoflagellates: flagellar gliding. www.cell.com/current-biol... - A 🧵
Reposted by Marvin Albert
We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
September 4, 2025 at 4:07 PM
We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Reposted by Marvin Albert
Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects!
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
iPortfolio Bootstrap Template - Index
acorbat.github.io
August 26, 2025 at 2:54 PM
Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects!
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.
Check out my portfolio and contact:
acorbat.github.io
Reposted by Marvin Albert
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 🧵)
📅 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 🧵)
August 25, 2025 at 9:07 AM
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 🧵)
📅 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 🧵)