Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...
π¬π€ As pre-announced a few days ago... please let us proudly present to you: π΄πππππππππ - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. π¬
doi.org/10.1101/2025...
Like β€οΈ, repost π, and most importantly... please send feedback βοΈ our way! π
We're hiring! Our IT Team is looking for a Linux Systems Engineer to support scientific computing and big data management. Apply here: www.fmi.ch/education-ca...
06.02.2025 13:29 β π 5 π 8 π¬ 0 π 0
2025 is now well underway and we are happy to announce that ZIDAS is coming to Basel this year !
2025.zidas.org
π Zarr-Python 3 is here! π
- Full support for Zarr v3 spec
- Chunk-sharding for more efficient data storage
- Major performance boosts with async I/O & parallel compression
π» pip install --upgrade zarr
π» conda install --channel conda-forge zarr
Blog post: https://buff.ly/3C3OwYw
I created a starter pack for Imaging Scientists that work in core facilities.
I'm sure I missed lots of people since I searched for those that have "core" or "facility" in their bios, so let me know who else should be added!
go.bsky.app/2bbgRQU
Nice! Can you add me too?
07.12.2024 17:00 β π 0 π 0 π¬ 1 π 0Quick reminder that we are looking for #TheoryFellow s to join us at @hhmijanelia.bsky.social. The deadline for applications is 1736280000.
01.12.2024 23:43 β π 4 π 2 π¬ 0 π 0
My #BioimageTooloftheDay
is the fantastic Introduction to Bioimage Analysis book by Pete Bankhead
bioimagebook.github.io/index.html
Because seriously, this is awesome
Also how can you get started without a good book
Dear blue-friends,
I have just learnt that, due to a cold and brutal administrative decision completely beyond my control, we have to terminate the contract of one of my PhD students, who was recently recruited for a project in cellular mechanobiology π².
Thread ! π
Congratulations! π₯
27.11.2024 08:05 β π 1 π 0 π¬ 0 π 0
We are looking for a Data Scientist at the MBExC Excellence Cluster in GΓΆttngen: shorturl.at/Jln3V .
Please RT! Read on for more details.
π¬ Join FMI! Weβre seeking a proteomics expert to develop cutting-edge mass spectrometry applications. Collaborate with top researchers in Genome Regulation, Multicellular Systems, and Neurobiology.
Apply now or share this job ad in your network!
#proteomics #CoreFacility
www.fmi.ch/education-ca...
βοΈπ
20.11.2024 11:37 β π 0 π 0 π¬ 0 π 0
A working example can be found here:
fmi-faim.github.io/example-proj...
From an end-user perspective I find pixi very simple, especially if one uses pixi-tasks. A standard execution pipeline now boils down to:
1. WD=runs/dataset pixi run build_config
2. WD=runs/dataset pixi run workflow
3. WD=runs/dataset pixi run visualization
No conda env create, conda activate...
Interested in microscopy and/or image analysis? Check out my newest starter pack of super folks.(which also links to the previous, 150-awesome-full one! Both also link to other imaging-y starter packs as I find them)
go.bsky.app/MU8c2A2
I made a BioImage Analysts Starter pack. Reachout if you're missing on it π¬π»π
go.bsky.app/2hPEBDu
βοΈ
Thank you!
So exciting to see everyone here. A brief self-intro for others:
I am currently a PhD student with @florianjug.bsky.social. My work involves the application of AI in bioimage analysis. I am interested in the application of #GenAI to solve inverse problems with #DiffusionModels #FlowMatching #VAEs.
