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C1M2: a universal algorithm for 3D instance segmentation, annotation, and quantification of irregular cells.

Hao Zheng1, Songlin Huang1,2, Jing Zhang1

  • 1Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.

Science China. Life Sciences
|May 27, 2023
PubMed
Summary
This summary is machine-generated.

A new algorithm, Crop Once Merge Twice (C1M2), accurately segments packed cells in 3D microscope images. This method also quantifies fluorescence intensity for advanced tissue cytometry and histopathological assays.

Keywords:
3D instance segmentationfluorescence imagesfluorescence intensityirregular cellsneural networkstissue cytometry

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Area of Science:

  • Biomedical imaging
  • Computational biology
  • Cell biology

Background:

  • Cell instance segmentation is vital for analyzing cellular morphology in 3D microscopy.
  • Existing 2D methods struggle with irregular cell shapes in 3D images.
  • Accurate 3D cell segmentation is crucial for quantitative biological analysis.

Purpose of the Study:

  • To develop a universal algorithm for accurate 3D cell instance segmentation.
  • To enable quantification of fluorescence intensity and expression levels in individual cells.
  • To establish a novel approach for 3D histopathological assays.

Main Methods:

  • Introduction of the Crop Once Merge Twice (C1M2) algorithm, a morphology-based approach.
  • C1M2 processes various 3D image types without requiring nucleus images.
  • Extension of C1M2 for quantifying fluorescence intensity of proteins and antibodies.

Main Results:

  • C1M2 achieves high segmentation accuracy for irregular cells in 3D images.
  • The algorithm successfully quantifies fluorescence intensity and annotates expression levels.
  • Demonstrated C1M2's capability for tissue cytometry in 3D histopathological assays.

Conclusions:

  • C1M2 offers a universal solution for 3D cell instance segmentation.
  • The algorithm provides essential spatial localization and morphological information.
  • C1M2 advances quantitative analysis in biological and histopathological studies.