#cellpose — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #cellpose, aggregated by home.social.
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Tried the same with a more realistic 3D stack from the #ImageJ sample library.#Cellpose runs fast and segments very well out of the box.#CellSeg3D takes considerably longer and seems to segment decently, but I couldn’t get a proper instance #segmentation in the post-processing step (which is recommended as part of its workflow). However, #CellSeg3D looks very promising — just needs some more time and parameter exploration, I guess.
I’d recommend giving it a try 👌
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Tried the same with a more realistic 3D stack from the #ImageJ sample library.#Cellpose runs fast and segments very well out of the box.#CellSeg3D takes considerably longer and seems to segment decently, but I couldn’t get a proper instance #segmentation in the post-processing step (which is recommended as part of its workflow). However, #CellSeg3D looks very promising — just needs some more time and parameter exploration, I guess.
I’d recommend giving it a try 👌
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Tried the same with a more realistic 3D stack from the #ImageJ sample library.#Cellpose runs fast and segments very well out of the box.#CellSeg3D takes considerably longer and seems to segment decently, but I couldn’t get a proper instance #segmentation in the post-processing step (which is recommended as part of its workflow). However, #CellSeg3D looks very promising — just needs some more time and parameter exploration, I guess.
I’d recommend giving it a try 👌
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Tried the same with a more realistic 3D stack from the #ImageJ sample library.#Cellpose runs fast and segments very well out of the box.#CellSeg3D takes considerably longer and seems to segment decently, but I couldn’t get a proper instance #segmentation in the post-processing step (which is recommended as part of its workflow). However, #CellSeg3D looks very promising — just needs some more time and parameter exploration, I guess.
I’d recommend giving it a try 👌
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Tried the same with a more realistic 3D stack from the #ImageJ sample library.#Cellpose runs fast and segments very well out of the box.#CellSeg3D takes considerably longer and seems to segment decently, but I couldn’t get a proper instance #segmentation in the post-processing step (which is recommended as part of its workflow). However, #CellSeg3D looks very promising — just needs some more time and parameter exploration, I guess.
I’d recommend giving it a try 👌
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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.
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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.
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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.
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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.
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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.
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✍️ 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.
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✍️ 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.
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✍️ 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.
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✍️ 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.
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✍️ 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.
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🤖 How resilient are deep learning models to real-world imperfections in microscopy?
🔗 Practical guidelines for cell segmentation models under optical aberrations in microscopy. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.09.002
📚 CSBJ Quantum Biology and Biophotonics: https://www.csbj.org/qbio
#CellSegmentation #Microscopy #AIinBiology #OpticalAberrations #DeepLearning #BiomedicalAI #Cellpose #ComputationalBiology #PLCM
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Cell/nuclei segmentation by training deep learning models for #CellPose and #StarDist incrementally, using sparse annotations
Latest work by Ko Sugawara, initiated in our team and completed at RIKEN
https://www.biorxiv.org/content/10.1101/2023.06.13.544786v1.full.pdf
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Cell/nuclei segmentation by training deep learning models for #CellPose and #StarDist incrementally, using sparse annotations
Latest work by Ko Sugawara, initiated in our team and completed at RIKEN
https://www.biorxiv.org/content/10.1101/2023.06.13.544786v1.full.pdf
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Cell/nuclei segmentation by training deep learning models for #CellPose and #StarDist incrementally, using sparse annotations
Latest work by Ko Sugawara, initiated in our team and completed at RIKEN
https://www.biorxiv.org/content/10.1101/2023.06.13.544786v1.full.pdf
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Can chatGPT also answer github issues for me? :ablobpeek: #cellpose
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Can chatGPT also answer github issues for me? :ablobpeek: #cellpose
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Can chatGPT also answer github issues for me? :ablobpeek: #cellpose
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Can chatGPT also answer github issues for me? :ablobpeek: #cellpose
