Segment Anything for Microscopy

Accurate segmentation of objects in microscopy images remains a bottleneck for many researchers despite the number of tools developed for this purpose. Here, we present Segment Anything for Microscopy (μSAM), a tool for segmentation and tracking in multidimensional microscopy data. It is based on Segment Anything, a vision foundation model for image segmentation. We extend it by fine-tuning generalist models for light and electron microscopy that clearly improve segmentation quality for a wide range of imaging conditions. We also implement interactive and automatic segmentation in a napari plugin that can speed up diverse segmentation tasks and provides a unified solution for microscopy annotation across…

• DF
  Deutsche Forschungsgemeinschaft

  Awards: EXC 2067/1-390729940, EXC 2067, 390729940, 2067/1-390729940, EXC 2067/1, 4341/2-1, PA 4341/2-1
• MU
  Monash University
• GG
  Georg-August-Universität Göttingen
• DK
  Deutsche Krebshilfe

  Award: 70115444
• RF
  Rheinische Friedrich-Wilhelms-Universität Bonn