Some impressions from last time
(We had a good time, and aim for it again.)
Organized with the great @biaunit.bsky.social , @gaellel.bsky.social and the IAH team.
09.03.2026 16:23
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Some impressions from last time
(We had a good time, and aim for it again.)
Organized with the great @biaunit.bsky.social , @gaellel.bsky.social and the IAH team.
Let's get ready for a full month of training in image analysis in @pasteur.fr , this summer!
Are you interested in learning how to do bioimage analysis? For light microscopy? for cryo-EM? And for cellular cryo-EM?
Stay tuned, Pasteur offers access to THREE courses, this June.
👇🎓
Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context.
Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).
A brief 🧵 (carried over from the old place)
A cochlea imaged in light-sheet microscopy (right) with staining for spiral ganglion neurons (red) and inner hair cells (blue). You will develop AI-based methods to analyze these structures, for example via segmentation of the individual cells (right) that will support gene therapy development for hearing loss and a better overall understanding of the anatomy of hearing.
Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx
Part of sfb1690.uni-goettingen.de to study hearing, vision, and more.
Plus, you can create pretty pictures as the one below :).
Drawing of the "Aeon" project, an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales.
Are you a neuroscientist with great coding skills, or a software engineer interested in the brain?
We are recruiting for a research software engineer to help us build pipelines to process weeks of neural and behavioural recordings from freely moving animals.
More details: bit.ly/rse-2026a
Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels. #ImageJ #Fiji #BigDataViewer
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).
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/...
🚨 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...
🚨 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!
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!
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-...
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...
📣 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...
