Marvin Albert

Research Software Engineer - Spatial-omics The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...

We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework.

We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community.

🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

https://doi.org/10.5281/zenodo.14762435 https://bsky.app/profile/falk-illustrations.de

AMAZING JOB OPPORTUNITY ALERT!!!

@calm-stp.bsky.social is hiring a Data & Systems Steward! 🧬

🔹Manage #bioimage data & #OMERO admin
🔹Automate via #Python/#Bash
🔹Support #FAIR principles
🔹Work closely with @crick-ia-team.bsky.social

⏰ Deadline: 08 Feb 2026

Apply: www.crick.ac.uk/careers-stud...

#teamtomo gets another quantitative cell biology tool!

We extend our Surface Morphometrics pipeline to measure membrane thickness.

Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).

Scientific Workflows Developer The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...

Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Our research scientist Núria Ros-Rocher won the 1st prize @zeiss-microscopy.bsky.social microscopy contest with this beautiful choano colony www.zeiss.fr/microscopie/... 🥳

C. flexa might not yet be a genetic model, but it is now at least a calendar model, which counts for something. I think.

The #CBIAS2025 poster collection is now available, along with associated DOIs for further dissemination. Take a look!

crick.figshare.com/collections/...

Deep Learning for Microscopy Image Analysis Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,

🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?

20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026

✍️ Jan 15 2026 ✍️

🔁 pls!!

www.janelia.org/you-janelia/...

I will be recruiting two postdocs early next year.
- One image analyst
- one biologist interested in working on lymphatics!

Reach out if you are interested 👍

Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff:

Paper: doi.org/10.1242/jcs....
Code: github.com/pertzlab/arc...
Plugin: github.com/pertzlab/arc...

I was invited by @focalplane.bsky.social to write a short description about it:

focalplane.biologists.com/2025/12/12/a...

Interview de chercheur-ses pour doc radio À l'occasion d'un projet de documentaire radio sur France Culture, je cherche des chercheur-ses représentant une diversité de disciplines mais également de statuts à interviewer. L'idée est de partir...

🚨 Je cherche des chercheur-ses de toutes disciplines pour un doc radio pour parler de leur sujet de recherche mais aussi de leur quotidien (une journée type au labo). Contrainte supplémentaire, le labo doit être hors de Paris.
Plus d'infos : forms.gle/hw9wH2p5UH4A...

Paris 13eme now.

BIOIMAGE ANALYSTS ASSEMBLE!!!

#CBIAS2025

TrackMate now integrates even more cutting-edge detection, segmentation and tracking methods and makes them fun and easy to use!

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!

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...

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...

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!

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.

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...

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...

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...

📢 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...

📣 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...

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.

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.

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)

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.

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 - 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

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)

Flyer for the Open Bioimaging Practices Meetups. 1. September 24th at 4pm: Guest presentation by Charlotte Soneson & Silvia Barbiero 2. October 28th at 4pm: Guest presentation by Marvin Albert 3. November 26th at 4pm: Guest presentations by Giliane Rochat & Flurin Sturzenegger

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)

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...

🚨 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...