4/14🔬 We captured 16-to 22-hour 3D movies of this process. However, segmenting and tracking individual cells in a dense 3D tissue is a challenging task. We built a deep learning pipeline that combines the forces of #StarDist, #UNET, #Cellpose, and #TrackMate. 💪#ImageAnalysis
Raw image (3D)
Cellpose segmentation and applied parameters
CellSeg_3D segmentation and applied parameters
CellSeg_3D post-hoc instant segmentation and applied parameters
Tested both tools also on a more realistic 3D stack from the #ImageJ sample library. #Cellpose is fast and works well out of the box. #CellSeg3D is, however, slower and needs some further tuning for instance segmentation I guess — but looks promising! Definitely worth a try 👌 #BioimageAnalysis
3D view: raw data (upper left), Cellpose segmentation (upper right), CellSeg3D segmentation (lower left)
Cellpose segmentation and applied parameters
CellSeg_3D segmentation and applied parameters
Tested #CellSeg3D and #Cellpose on their example c5image dataset. Both segmentations look reasonable out-of-the-box, without any deep parameter tuning. With some extra effort, one could likely push either further I guess. Overall, both tools perform quite well on this small sample data set.
✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later.
@napari.org
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel
We should also start this discussion on image.sc
#cellpose #imageanalysis #image.sc #fiji #imagej
We were already using #cellpose to segment kidney tubules but this combination with SAM should make it even more generalizable and powerful! Very exciting!
Bring your samples into focus! A new version of the #Cellpose cell boundary mapping tool, developed at @hhmijanelia.bsky.social by @computingnature.bsky.social and @marius10p.bsky.social, now works on less-than-perfect microscopy images that are noisy, blurry, or undersampled.
🖥️ A new version of #Cellpose – the popular tool developed by @computingnature.bsky.social & @marius10p.bsky.social that maps the boundaries of diverse cells in microscopy images – now works on less-than-perfect pictures that are noisy, blurry, or undersampled.
🔗 www.janelia.org/news/newest-...
New tutorial on analyzing organoid screening datasets with Python! Covers preprocessing, Cellpose segmentation, and ANOVA for statistical validation. Free code included.
Watch here: youtu.be/KI_zNWASTqg
#python #drugdiscovery #bioimageanalysis #microscopy #organoids #Cellpose
The image segmentation tools & training of ML/DL models used to generate data in the talk were prepared thanks to manual and training notes by Cameron Nowel, all available at #zerocostAI here: 👇👇
sites.google.com/monash.edu/fij…
#AIinInfectiousDiseases #OpenAI #APMC13 #LABKIT #Ilastik #CellPose
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
only took me 4 hours this time to get all dependencies sorted out to run #cellpose in #cellprofiler. Documentation is great for both, but every system I install this on has it's own set of problems to get started. sigh.
We took a “no cell shall be left behind” approach which wouldn’t be possible without #Cellpose, #TrackMate by @jytinevez.bsky.social , #Fiji and #rstats analysis and visualization with GlmmTMB, emmeans and #SuperPlots and microscopy cores at UCSD. Plasmids available from @addgene.bsky.social
#MicroscopeMonday by Raphael
for our first post on bluesky here's our new image processing available on our OpenCID database: you can now directly run #denoise #deblur #upsample with the new version of cellpose on all your images
thanks to the #cellpose team for their always top-notch dev
Subcellular #SpatialTranscriptomics Cell Segmentation
#TransformerNeuralNetwork
based on Image AND Transcriptome
For Single-Cell/Subcellular ST
Stereo-seq; Seq-scope
vs other #DeepLearning methods #StarDist #CellPose #DeepCell
#NatureMethods 2023
www.nature.com/articles/s41...
