Today I would like to highlight one of our favorite DL-segmentation network: StarDist by @maweigert.bsky.social and colleagues. In my lab we love and use StarDist all the time
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
GitHub - stardist/stardist: StarDist - Object Detection with Star-convex Shapes
StarDist - Object Detection with Star-convex Shapes - stardist/stardist
github.com
November 14, 2024 at 3:34 PM
Today I would like to highlight one of our favorite DL-segmentation network: StarDist by @maweigert.bsky.social and colleagues. In my lab we love and use StarDist all the time
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
github.com/stardist/sta...
link.springer.com/chapter/10.1...
#BioimageTooloftheDay
Tittade in på bokförsäljningsrapporten på Stardist (f.d. Stjärndistribution) och jösses vad folk beställt Medley Rewind på sistone!
Inget gör mig gladare, men... vadan detta? Hurra! Va?
Inget gör mig gladare, men... vadan detta? Hurra! Va?
September 29, 2025 at 12:07 PM
Tittade in på bokförsäljningsrapporten på Stardist (f.d. Stjärndistribution) och jösses vad folk beställt Medley Rewind på sistone!
Inget gör mig gladare, men... vadan detta? Hurra! Va?
Inget gör mig gladare, men... vadan detta? Hurra! Va?
StarDistによる細胞の自動セグメンテーション。以前は背景輝度均して閾値設定してパーティクル数えて…とやってましたが、あの苦労はなんだったのだろうかと😂
github.com/stardist/sta...
github.com/stardist/sta...
GitHub - stardist/stardist: StarDist - Object Detection with Star-convex Shapes
StarDist - Object Detection with Star-convex Shapes - GitHub - stardist/stardist: StarDist - Object Detection with Star-convex Shapes
github.com
February 10, 2024 at 4:37 AM
StarDistによる細胞の自動セグメンテーション。以前は背景輝度均して閾値設定してパーティクル数えて…とやってましたが、あの苦労はなんだったのだろうかと😂
github.com/stardist/sta...
github.com/stardist/sta...
✍️ 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
@napari.org
New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis -
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
Self-supervised, label-free 3D cell imaging is here
EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...
actu.epfl.ch
July 11, 2025 at 1:58 PM
✍️ 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
@napari.org
Led by António Brito and Bruno Saraiva, with Dominik Alwardt, Beatriz de P. Mariz, Sérgio Filipe and @pinholab.bsky.social, at @itqbnova.bsky.social. Built on @napari.org: StarDist, Cellpose and U-Net, plus a retrainable classifier =)
September 15, 2026 at 9:18 AM
Led by António Brito and Bruno Saraiva, with Dominik Alwardt, Beatriz de P. Mariz, Sérgio Filipe and @pinholab.bsky.social, at @itqbnova.bsky.social. Built on @napari.org: StarDist, Cellpose and U-Net, plus a retrainable classifier =)
Contributing to this project has been very cool!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Just before the holidays, here is the latest from the Oricchio lab. In collaboration with the hemato-oncology team, we established a new model to test therapies on lymphoma patient samples by preserving the tissue composition and architecture of the original tumors. www.nature.com/articles/s41...
Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening - Nature Communications
Choosing the most effective anti-cancer therapy is difficult due to the high degree of tumour cell and tumour microenvironment heterogeneity. Here, the authors develop a platform for the generation of...
www.nature.com
December 18, 2024 at 3:10 PM
Contributing to this project has been very cool!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Try it yourself! The plugin, documentation, and example datasets are available at:
multichannel-nuclear-analysis.github.io
Special thanks to the StarDist team for their incredible segmentation algorithm that made this possible.
#ImageAnalysis #FIJI #ImageJ #Microscopy
multichannel-nuclear-analysis.github.io
Special thanks to the StarDist team for their incredible segmentation algorithm that made this possible.
#ImageAnalysis #FIJI #ImageJ #Microscopy
Multichannel Nuclear Analysis plugin
An ImageJ/FIJI plugin for analyzing multi-channel fluorescence images with a focus on nuclear segmentation using StarDist. https://multichannel-nuclear-analysis.github.io/
multichannel-nuclear-analysis.github.io
June 7, 2025 at 2:41 PM
Try it yourself! The plugin, documentation, and example datasets are available at:
multichannel-nuclear-analysis.github.io
Special thanks to the StarDist team for their incredible segmentation algorithm that made this possible.
#ImageAnalysis #FIJI #ImageJ #Microscopy
multichannel-nuclear-analysis.github.io
Special thanks to the StarDist team for their incredible segmentation algorithm that made this possible.
#ImageAnalysis #FIJI #ImageJ #Microscopy
🔥 In one test (500-frame light-sheet dataset), Ultrack reduced manual corrections by >2× !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
August 25, 2025 at 9:06 AM
🔥 In one test (500-frame light-sheet dataset), Ultrack reduced manual corrections by >2× !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
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
September 22, 2025 at 9:37 AM
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
Qupath + Cellpose + Stardistで細胞質と核をsegmentaionめっちゃ綺麗にできて、細胞ごとにデータ得られる！すごすぎ！
June 15, 2024 at 6:13 AM
Qupath + Cellpose + Stardistで細胞質と核をsegmentaionめっちゃ綺麗にできて、細胞ごとにデータ得られる！すごすぎ！
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 😀
Here some individual references:
IJ-wrapper: github.com/BIOP/ijl-uti...
cellpose (cellpose.readthedocs.io/en/latest/)
omnipose (github.com/kevinjohncut...)
Stardist (github.com/stardist/sta...)
IJ-wrapper: github.com/BIOP/ijl-uti...
cellpose (cellpose.readthedocs.io/en/latest/)
omnipose (github.com/kevinjohncut...)
Stardist (github.com/stardist/sta...)
GitHub - BIOP/ijl-utilities-wrappers: Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)
Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display) - BIOP/ijl-utilities-wrappers
github.com
November 17, 2024 at 8:05 AM
Here some individual references:
IJ-wrapper: github.com/BIOP/ijl-uti...
cellpose (cellpose.readthedocs.io/en/latest/)
omnipose (github.com/kevinjohncut...)
Stardist (github.com/stardist/sta...)
IJ-wrapper: github.com/BIOP/ijl-uti...
cellpose (cellpose.readthedocs.io/en/latest/)
omnipose (github.com/kevinjohncut...)
Stardist (github.com/stardist/sta...)
Konstaterar att det börjar bli läge för ett tilltryck av Tobias Hadins uppskattade zombierollspel "Skjut dom i huvudet". Låga lager hos våra distributörer Stardist och Omnix samt även i Vildhallons webshop. Kul som bara den!
March 19, 2025 at 7:30 PM
Konstaterar att det börjar bli läge för ett tilltryck av Tobias Hadins uppskattade zombierollspel "Skjut dom i huvudet". Låga lager hos våra distributörer Stardist och Omnix samt även i Vildhallons webshop. Kul som bara den!
🔬🚀 Out now in Communications AI & Computing: mAIcrobe, our open-source napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇
doi.org/10.1038/s44488-026-00022-y
doi.org/10.1038/s44488-026-00022-y
September 15, 2026 at 9:18 AM
🔬🚀 Out now in Communications AI & Computing: mAIcrobe, our open-source napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇
doi.org/10.1038/s44488-026-00022-y
doi.org/10.1038/s44488-026-00022-y
If you've used Cellpose, StarDist, Hover-Net or Omnipose, the intermediate representation (masks, contours, distances, affinities, embeddings) drives everything — yet it's never been fairly compared.
597 preregistered experiments, 6 heterogeneous datasets, 2D & 3D, fully open via BiaPy. (2/3)
597 preregistered experiments, 6 heterogeneous datasets, 2D & 3D, fully open via BiaPy. (2/3)
June 30, 2026 at 12:30 PM
If you've used Cellpose, StarDist, Hover-Net or Omnipose, the intermediate representation (masks, contours, distances, affinities, embeddings) drives everything — yet it's never been fairly compared.
597 preregistered experiments, 6 heterogeneous datasets, 2D & 3D, fully open via BiaPy. (2/3)
597 preregistered experiments, 6 heterogeneous datasets, 2D & 3D, fully open via BiaPy. (2/3)
#BIAToolTip No.2
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
November 17, 2024 at 8:05 AM
#BIAToolTip No.2
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
Today, I would like to highlight the amazing IJ-wrapper 😎 for cellpose, omnipose and StarDist and more from
@romainguiet.bsky.social
and colleagues. It allows seamless integration of DL tools in a Fiji batch workflow including all imgae pre- and post-processing and analysis steps.
#Microscopy folk: If Stardist has stopped working for you since the recent update, reset the tensor flow update site on FIJI!
January 30, 2025 at 5:25 PM
#Microscopy folk: If Stardist has stopped working for you since the recent update, reset the tensor flow update site on FIJI!
Day 3️⃣ of our @embo.org course on "Advanced methods in bioimage analysis" at @embl.org with "Practical session 3: Tracking" 🔬🦠🔀.
@jytinevez.bsky.social is already shining at the stage! 🕺🪩.
Important update: #TrackMate v8 is coming! 🤗
@jytinevez.bsky.social is already shining at the stage! 🕺🪩.
Important update: #TrackMate v8 is coming! 🤗
September 16, 2025 at 8:10 AM
Day 3️⃣ of our @embo.org course on "Advanced methods in bioimage analysis" at @embl.org with "Practical session 3: Tracking" 🔬🦠🔀.
@jytinevez.bsky.social is already shining at the stage! 🕺🪩.
Important update: #TrackMate v8 is coming! 🤗
@jytinevez.bsky.social is already shining at the stage! 🕺🪩.
Important update: #TrackMate v8 is coming! 🤗
ha-ha 🤣 ma tean jällegi tüüpi, kes firma suvekatel tegi rattamatka, millest ta ise osa ei võtnud, stardist samuti 2 klõpsu. ratturid startisid organiseeritule hanerivvi, et kõik ikka kaadrisse jääks. ka jäädvustamise koht sai hoolikalt valitud.
May 3, 2026 at 10:59 AM
ha-ha 🤣 ma tean jällegi tüüpi, kes firma suvekatel tegi rattamatka, millest ta ise osa ei võtnud, stardist samuti 2 klõpsu. ratturid startisid organiseeritule hanerivvi, et kõik ikka kaadrisse jääks. ka jäädvustamise koht sai hoolikalt valitud.
Q2 Did you use the tensorflow version of your semantic segmentation notebooks? Any plans to move to Pytorch? (I know you guys set up a lot of things on the cloud, but for Windows Users the tensor flow (and stardist) installation is becoming increasingly convoluted.
May 1, 2025 at 7:03 PM
Q2 Did you use the tensorflow version of your semantic segmentation notebooks? Any plans to move to Pytorch? (I know you guys set up a lot of things on the cloud, but for Windows Users the tensor flow (and stardist) installation is becoming increasingly convoluted.
Oh that's a good call. His turn in Stardist hinted at what a good fit he'd be
January 29, 2026 at 8:47 PM
Oh that's a good call. His turn in Stardist hinted at what a good fit he'd be
Bowie's 5th album, this introduced the world to his alter ego Ziggy Stardist.
Before today, I'd only heard some songs here and there from different compilation albums. Feels good to finally sit down and listen to this front-to-back
Before today, I'd only heard some songs here and there from different compilation albums. Feels good to finally sit down and listen to this front-to-back
July 25, 2025 at 3:22 PM
Bowie's 5th album, this introduced the world to his alter ego Ziggy Stardist.
Before today, I'd only heard some songs here and there from different compilation albums. Feels good to finally sit down and listen to this front-to-back
Before today, I'd only heard some songs here and there from different compilation albums. Feels good to finally sit down and listen to this front-to-back
We built StarDist to detect cells in volumetric microscopy and jointly infer closed curved parametric surfaces for each cell. It's an example of an interpretable machine learning approach. More detail in the blog post and preprint.
www.focolab.org/post/surfdis...
www.focolab.org/post/surfdis...
"SurfDist" pre-print posted
We developed an "interpretable machine learning" system to find and characterize blobs in volumetric images, such as microscopy images of cells, something we need to do all the time in our lab. The no...
www.focolab.org
July 14, 2025 at 6:16 PM
We built StarDist to detect cells in volumetric microscopy and jointly infer closed curved parametric surfaces for each cell. It's an example of an interpretable machine learning approach. More detail in the blog post and preprint.
www.focolab.org/post/surfdis...
www.focolab.org/post/surfdis...
Love to hear more about testing. I'm always skeptical when I hear "new method B" outperforms previous method "A" because it often turns out "A" was not run optimally. Seems reasonable in an unsupervised or general mode this new method could be better than generalist Stardist/Cellpose but ...
July 12, 2025 at 1:49 PM
Love to hear more about testing. I'm always skeptical when I hear "new method B" outperforms previous method "A" because it often turns out "A" was not run optimally. Seems reasonable in an unsupervised or general mode this new method could be better than generalist Stardist/Cellpose but ...
Overall, I rank Stardist Memory at a pretty solid A tier. People kept saying it was gonna drop the ball on the last episode, but honestly I don't see it? Sure, Nina acted incomprehensibly in the colony, but I feel like it was the writers trying to say something rather than bad writing.
June 24, 2025 at 1:48 AM
Overall, I rank Stardist Memory at a pretty solid A tier. People kept saying it was gonna drop the ball on the last episode, but honestly I don't see it? Sure, Nina acted incomprehensibly in the colony, but I feel like it was the writers trying to say something rather than bad writing.