23 Dec 2024
🥳Alrighty - end-of-year push to get the final version of #CellSeg3D out!
👩💻 pip install napari-cellseg3d==0.2.2
📚 biorxiv.org/content/10.1101/…
We extended benchmarking, new videos, extended text, and a demo on cFOS 👋
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31 Oct 2024
Of Your Gourd:🎃Self-supervised learning approach CellSeg3D for fluorescence microscopy quantifies cells in 3D volumes (as from this human brain)
📷: @AChRD4 et al @mwmathislab @EPFL in @elife preprint
➡️: bpod.org.uk/archive/2024/10/…
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10 Sep 2024
Again, many thanks to the awesome #CellSeg3D team (on X) ❤️ @AChRD4 @TheVetFuturist @CYHSM @vmaxmc2 @itsasimiqbal @stephane_pages @SebHausmann 🎉🔥💻🦄
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10 Sep 2024
#CellSeg3D hits 85K downloads, and we’ve updated our preprint to add a few more key details and added new demo videos 🎥!
Check out the demos from @AChRD4 and @SebHausmann 🔥
youtu.be/3UOvvpKxEAo?feature…
m.youtube.com/watch?v=U2a9Ib…
biorxiv.org/content/10.1101/…
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Happy birthday @napari_imaging - you’ve been a game changer, including for us: @DeepLabCut and #CellSeg3D 👏🙏🏼🎉
3 Jun 2024
6 years ago to the minute 🥳🎂, napari co-founder @loicaroyer made the 1st commit to the “napari-core” repo.
github.com/napari/napari-cor…
Since then, over 150 community members have contributed to the napari code, docs, & tooling, and over 400 plugins have been developed. #napariAt6
ALT git log output in a terminal showing the timestamp of the first commit to napari(-core)
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18 May 2024
#CellSeg3D in bioRxiv 🎉
Lead by @AChRD4👏, this self-supervised 3D cell segmentation Python package with @napari_imaging plugin is a game-changer🔬
Proud to have kickstarted this project with @TrackingActions during my postdoc at @EPFL_en - amazing to see how far it has come🚀
18 May 2024
🎉 new preprint posted of potential interest, lead by talented masters student @AChRD4:
🔥fully unsupervised 3D cell segmentation that is as good (or better) than leading supervised methods, with @napari_imaging integration! 👏
biorxiv.org/content/10.1101/…
➕new 3D GT dataset ⬇️🧵
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18 May 2024
CellSeg3D: self-supervised 3D cell segmentation for microscopy biorxiv.org/cgi/content/shor… #biorxiv_cellbio
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18 May 2024
CellSeg3D: self-supervised 3D cell segmentation for microscopy biorxiv.org/cgi/content/shor… #bioRxiv
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Maybe try cellseg3D? If in 3D ;) github.com/AdaptiveMotorCont…
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Have you tried #CellSeg3D yet for automating your 3D lightsheet microscopy analysis?
We just hit >75K pip installations! 🥳
We have some 🔥 coming soon ... but in the meantime, github.com/AdaptiveMotorCont… lead by @AChRD4 @Neuro_X_EPFL
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Also check out our CellSeg3D project ;) github.com/AdaptiveMotorCont…
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Learn more about #Cellseg3D : github.com/AdaptiveMotorCont…
And about #BrainReg from @brain_globe : github.com/brainglobe/brainr…
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Legos or 🐭 brain? 🧠 🧱
@AChRD4 is working on seamless integration of @brain_globe #BrainReg with #cellseg3D 🔥🚧✨data courtesy of our awesome collaborators at the @Wysscenter @stephane_pages #openScience
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30 Aug 2022
And Cyril aka @AChRD4 joins Twitter! 🎉
Follow him for excellent updates on our rapidly developing 3D cell segmentation computer vision work! He is the lead developer of #CellSeg3D
21 Jul 2022
#CLARITY @MesoSpim is amazing. We aim to directly do 3D semantic & instance segmentation on this data for cFOS, co-counting, etc.
My awesome lab members Cyril Achard & @vmaxmc2 built a @napari_imaging plugin to make a free, open source tool for this: github.com/AdaptiveMotorCont…
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26 Aug 2022
Sounds like a great workflow; would be happy for you to test out #cellseg3D, and if you have any open source 3D data for training, that would be amazing to share! github.com/AdaptiveMotorCont…
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21 Jul 2022
There is no paper, but check out the docs: adaptivemotorcontrollab.gith… and watch the project grow over the next year as we integrate with @brain_globe tools and beyond!
It is also on pypi as a release candidate & #napariHub:
pip install napari-cellseg3d
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