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
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
Annotating Images in Cellpose - FocalPlane
Annotating Images in Cellpose - How to
focalplane.biologists.com
June 9, 2025 at 9:43 AM
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
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
#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...
February 12, 2025 at 11:10 AM
#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...
Another outcome from the Appose processing hackathon:
Cellpose simple tile processing in Fiji, with #imglib2 and #appose only.
With @gaellel.bsky.social and @strigaud.bsky.social
Cellpose simple tile processing in Fiji, with #imglib2 and #appose only.
With @gaellel.bsky.social and @strigaud.bsky.social
May 28, 2026 at 5:35 PM
Another outcome from the Appose processing hackathon:
Cellpose simple tile processing in Fiji, with #imglib2 and #appose only.
With @gaellel.bsky.social and @strigaud.bsky.social
Cellpose simple tile processing in Fiji, with #imglib2 and #appose only.
With @gaellel.bsky.social and @strigaud.bsky.social
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 3, 2025 at 7:12 PM
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
CellPose 4.0 is a beast. Segmented human microglia, in brightfield. Credit to Sydney Houser.
September 11, 2025 at 1:34 PM
CellPose 4.0 is a beast. Segmented human microglia, in brightfield. Credit to Sydney Houser.
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try!
nimbusimage.com
nimbusimage.com
May 7, 2025 at 6:19 PM
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try!
nimbusimage.com
nimbusimage.com
My #BioimageTooloftheDay is an easy one: Cellpose by @computingnature.neuromatch.social.ap.brid.gy and colleagues
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
Cellpose 2.0: how to train your own model - Nature Methods
Cellpose 2.0 improves cell segmentation by offering pretrained models that can be fine-tuned using a human-in-the-loop training pipeline and fewer than 1,000 user-annotated regions of interest.
www.nature.com
November 15, 2024 at 4:40 PM
My #BioimageTooloftheDay is an easy one: Cellpose by @computingnature.neuromatch.social.ap.brid.gy and colleagues
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
An awesome DL-segmentation network to segment cells from microscopy images
www.nature.com/articles/s41...
When we do not use StarDist, we use Cellpose 😀
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.
Newest version of Cellpose can spot cell boundaries even in cloudy conditions
Picking out individual cells in distorted microscopy images is now as easy as clicking a button. A new version of Cellpose – the popular tool that maps the boundaries of diverse cells in microscopy
buff.ly
February 17, 2025 at 1:42 PM
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.
- new Cellpose 3 integration
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
November 20, 2025 at 11:42 AM
- new Cellpose 3 integration
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
Cellpose 3 is wonderful, easier to install and supports GPUs everywhere.
Thanks! Here's more info on cellpose-SAM for anyone interested bsky.app/profile/mari...
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 7, 2025 at 10:26 PM
Thanks! Here's more info on cellpose-SAM for anyone interested bsky.app/profile/mari...
Cellpose-SAM outperforms human-to-human agreement and approaches an estimated absolute bound on performance.
May 3, 2025 at 7:12 PM
Cellpose-SAM outperforms human-to-human agreement and approaches an estimated absolute bound on performance.
Everyone in the lab is raving about Cellpose-SAM. Segmenting the previously unsegmentable across a range of different cell types and markers.
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
June 23, 2025 at 2:32 PM
Everyone in the lab is raving about Cellpose-SAM. Segmenting the previously unsegmentable across a range of different cell types and markers.
We combined:
1) SAM, a pretrained foundation model with good generalization properties.
2) Cellpose, a good cellular segmentation framework.
1) SAM, a pretrained foundation model with good generalization properties.
2) Cellpose, a good cellular segmentation framework.
May 3, 2025 at 7:12 PM
We combined:
1) SAM, a pretrained foundation model with good generalization properties.
2) Cellpose, a good cellular segmentation framework.
1) SAM, a pretrained foundation model with good generalization properties.
2) Cellpose, a good cellular segmentation framework.
🖱️ Picking out individual cells in distorted microscopy images is now as easy as clicking a button, thanks to Cellpose3: www.janelia.org/news/newest-...
Newest version of Cellpose can spot cell boundaries even in cloudy conditions
Picking out individual cells in distorted microscopy images is now as easy as clicking a button. A new version of Cellpose – the popular tool that maps the boundaries of diverse cells in microscopy
www.janelia.org
May 9, 2025 at 1:22 PM
🖱️ Picking out individual cells in distorted microscopy images is now as easy as clicking a button, thanks to Cellpose3: www.janelia.org/news/newest-...
forum.image.sc/t/cellpose-3... Interesting forum question on 3D Cellpose that isn't answered yet. I played around a bit this morning but couldn't quite figure it out. Love to hear from others who work with 3D Cellpose (or other 3D segmentation methods)
December 4, 2024 at 2:34 PM
forum.image.sc/t/cellpose-3... Interesting forum question on 3D Cellpose that isn't answered yet. I played around a bit this morning but couldn't quite figure it out. Love to hear from others who work with 3D Cellpose (or other 3D segmentation methods)
- new version of the Cellpose integration (including Cellpose 3 & Cellpose-SAM)
- Omnipose - new
- YOLO - new
- Trackastra - new
- Spotiflow - new
- inTRACKtive - new
- Omnipose - new
- YOLO - new
- Trackastra - new
- Spotiflow - new
- inTRACKtive - new
November 20, 2025 at 11:42 AM
- new version of the Cellpose integration (including Cellpose 3 & Cellpose-SAM)
- Omnipose - new
- YOLO - new
- Trackastra - new
- Spotiflow - new
- inTRACKtive - new
- Omnipose - new
- YOLO - new
- Trackastra - new
- Spotiflow - new
- inTRACKtive - new
A lot happening for microscopy segmentation. Thanks for highlighting our paper and CellPose 3, Rita!
So much happening in the segmentation space for bioimage analysis. These two papers that were published online today really stood out to me as noteworthy (a thread).
February 12, 2025 at 6:22 PM
A lot happening for microscopy segmentation. Thanks for highlighting our paper and CellPose 3, Rita!
Reworked the Cellpose integration, and add Omnipose and Cellpose-SAM
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
November 20, 2025 at 11:42 AM
Reworked the Cellpose integration, and add Omnipose and Cellpose-SAM
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
The Cellpose integration has been rewritten in full. You will now find the following detectors:
- Omnipose
CellSAM
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
December 11, 2025 at 12:36 PM
CellSAM
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org
Outperforming CellPose
Similar to Human
Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation
@natmethods.nature.com 2025
www.nature.com/articles/s41...
Accessible and accurate cytometry analysis using fluorescence microscopes by Bo Huang and team:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 24, 2025 at 10:57 AM
Accessible and accurate cytometry analysis using fluorescence microscopes by Bo Huang and team:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
3D #SpatialMultiomics on the way!😍
Cycle Hybridization Chain Reaction
14 bp split L+R DNA barcodes
3 color channels
Cellpose-based 3D nucleus segmentation
120 RNA probes + 8 antibodies
~50 µm hippocampal slice
44 imaging cycles over 11 days
@science.org 2025
www.science.org/doi/10.1126/...
Cycle Hybridization Chain Reaction
14 bp split L+R DNA barcodes
3 color channels
Cellpose-based 3D nucleus segmentation
120 RNA probes + 8 antibodies
~50 µm hippocampal slice
44 imaging cycles over 11 days
@science.org 2025
www.science.org/doi/10.1126/...
March 20, 2025 at 10:44 AM
3D #SpatialMultiomics on the way!😍
Cycle Hybridization Chain Reaction
14 bp split L+R DNA barcodes
3 color channels
Cellpose-based 3D nucleus segmentation
120 RNA probes + 8 antibodies
~50 µm hippocampal slice
44 imaging cycles over 11 days
@science.org 2025
www.science.org/doi/10.1126/...
Cycle Hybridization Chain Reaction
14 bp split L+R DNA barcodes
3 color channels
Cellpose-based 3D nucleus segmentation
120 RNA probes + 8 antibodies
~50 µm hippocampal slice
44 imaging cycles over 11 days
@science.org 2025
www.science.org/doi/10.1126/...
🖥️ 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-...
🔗 www.janelia.org/news/newest-...
February 13, 2025 at 5:35 PM
🖥️ 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-...
🔗 www.janelia.org/news/newest-...
Cellpose: psychedelic version
May 29, 2026 at 9:28 AM
Cellpose: psychedelic version
I'm considering creating a video tutorial on bioimage analysis with PyImageJ, TrackMate, and Cellpose. It would focus on simplifying installation and include examples like multi-level tracking with single-cell and single-bacteria tracking within cells. Would anyone be interested?
November 26, 2024 at 1:30 AM
I'm considering creating a video tutorial on bioimage analysis with PyImageJ, TrackMate, and Cellpose. It would focus on simplifying installation and include examples like multi-level tracking with single-cell and single-bacteria tracking within cells. Would anyone be interested?
And in the latest release we have support for larger-than-memory datasets with Cellpose thanks to Greg Fleishman: cellpose.readthedocs.io/en/latest/di...
Big Data — cellpose 3.1.1.1-2-gdf96a99 documentation
cellpose.readthedocs.io
February 12, 2025 at 11:10 AM
And in the latest release we have support for larger-than-memory datasets with Cellpose thanks to Greg Fleishman: cellpose.readthedocs.io/en/latest/di...