Common cellular segmentation models based on machine learning perform suboptimally for test images that differ greatly from training images. Cellpose 2.0 allows biologists to quickly train state-of-the-art segmentation models on their own imaging data. This was previously only possible using large, annotated datasets and required expert machine learning knowledge.
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References
Boutros, M., Heigwer, F. & Laufer, C. Microscopy-based high-content screening. Cell 163, 1314–1325 (2015). A Review article that presents various image-based screening methods and the image analysis techniques required to interpret the data.
Caicedo, J. C. et al. Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nat. Methods 16, 1247–1253 (2019). This paper reports the results of the Data Science Bowl nuclear segmentation challenge, in which models trained on the most comprehensive image set performed best.
Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods 18, 100–106 (2021). This paper introduces the original Cellpose segmentation model and cellular dataset.
Greenwald, N. F. et al. Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat. Biotechnol. 40, 555–565 (2021). This paper introduces the Mesmer segmentation model and the TissueNet dataset, which contains over 1 million manually labeled cells from different tissues and fluorescent imaging platforms.
Edlund, C. et al. LiveCell—a large-scale dataset for label-free live cell segmentation. Nat. Methods 18, 1038–1045 (2021). This paper introduces the LiveCell dataset, which contains over 1.6 million manually labeled cells in phase contrast images from various cell culture lines.
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This is a summary of: Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat. Methods https://doi.org/10.1038/s41592-022-01663-4 (2022).
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A cellular segmentation algorithm with fast customization. Nat Methods 19, 1536–1537 (2022). https://doi.org/10.1038/s41592-022-01664-3
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DOI: https://doi.org/10.1038/s41592-022-01664-3