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Segment Anything for Microscopy

Nabeel Khalid
In: Nature, Vol. None, Pages 1-30, Nature Methods, 8/2024.


We present Segment Anything for Microscopy, a tool for interactive and automatic segmentation and tracking of objects in multi-dimensional microscopy data. Our method is based on Segment Anything, a vision foundation model for image segmentation. We extend it by training specialized models for microscopy data that significantly improve segmentation quality for a wide range of imaging conditions. We also implement annotation tools for interactive (volumetric) segmentation and tracking, that speed up data annotation significantly compared to established tools. Our work constitutes the first application of vision foundation models to microscopy, laying the groundwork for solving image analysis problems in these domains with a small set of powerful deep learning architectures.


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