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Self-supervised Dense Representation Learning for Live-Cell Microscopy with Time Arrow Prediction

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Medical Image Computing and Computer Assisted Intervention – MICCAI 2023 (MICCAI 2023)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 14227))

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State-of-the-art object detection and segmentation methods for microscopy images rely on supervised machine learning, which requires laborious manual annotation of training data. Here we present a self-supervised method based on time arrow prediction pre-training that learns dense image representations from raw, unlabeled live-cell microscopy videos. Our method builds upon the task of predicting the correct order of time-flipped image regions via a single-image feature extractor followed by a time arrow prediction head that operates on the fused features. We show that the resulting dense representations capture inherently time-asymmetric biological processes such as cell divisions on a pixel-level. We furthermore demonstrate the utility of these representations on several live-cell microscopy datasets for detection and segmentation of dividing cells, as well as for cell state classification. Our method outperforms supervised methods, particularly when only limited ground truth annotations are available as is commonly the case in practice. We provide code at

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We thank Albert Dominguez (EPFL) and Uwe Schmidt for helpful comments, Natalie Dye (PoL Dresden) and Franz Gruber for providing the Flywing dataset, Benedikt Mairhörmann and Kurt Schmoller (Helmholtz Munich) for providing additional Yeast training data, and Alan Lowe (UCL) for providing the Mdck dataset. M.W. and B.G. are supported by the EPFL School of Life Sciences ELISIR program and CARIGEST SA.

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Correspondence to Martin Weigert .

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Gallusser, B., Stieber, M., Weigert, M. (2023). Self-supervised Dense Representation Learning for Live-Cell Microscopy with Time Arrow Prediction. In: Greenspan, H., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2023. MICCAI 2023. Lecture Notes in Computer Science, vol 14227. Springer, Cham.

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