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SAMCell: Generalized label-free biological cell segmentation with segment anything.

Alexandra Dunnum VandeLoo1, Nathan J Malta2, Saahil Sanganeriya2

  • 1School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

Plos One
|September 8, 2025
PubMed
Summary

Automated cell segmentation using SAMCell, a modified Segment Anything Model (SAM), enhances cell health analysis in microscopy. This tool simplifies high-throughput cell culturing by providing high-quality segmentation with reduced technical expertise.

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Area of Science:

  • Cell Biology
  • Microscopy Imaging
  • Computational Biology

Background:

  • Assessing cell morphology, confluency, and growth is crucial for cell health analysis in microscopy.
  • Manual inspection of cell images is laborious for high-throughput applications.
  • Automated cell segmentation methods often require expertise and annotated datasets.

Purpose of the Study:

  • To develop an automated cell segmentation technique for microscopy images.
  • To reduce the technical expertise and labor required for cell analysis.
  • To improve the efficiency and quality of cell segmentation in high-throughput studies.

Main Methods:

  • Modified Meta's Segment Anything Model (SAM) into SAMCell.
  • Trained SAMCell on a large-scale dataset of diverse microscopy images.
  • Developed a user-friendly graphical user interface (UI) for the automated technique.

Main Results:

  • SAMCell effectively performs cell segmentation on various microscopy images, including unseen cell types.
  • The model demonstrates robustness across different microscopes and image acquisition conditions.
  • The user-friendly UI significantly lowers the technical barrier for automated microscopy.

Conclusions:

  • SAMCell provides higher quality automated cell segmentation compared to previous methods.
  • The graphical user interface streamlines the process, reducing manual labor in cell culturing.
  • This automated approach enhances the efficiency of biological research involving cell analysis.