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Updated: Jan 15, 2026

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
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Toggle-Untoggle - a cell segmentation tool with an interactive user verification interface.

Nina Grishchenko1, Margarita Byrsan2, Matthew Craig Drummond-Stoyles3

  • 1Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada.

Journal of Cell Science
|October 9, 2025
PubMed
Summary
This summary is machine-generated.

Toggle-Untoggle is a new desktop application for easy quality control of automated cell segmentation in microscopy images. This code-free tool enhances accuracy and efficiency for single-cell analysis, making advanced techniques accessible to more researchers.

Keywords:
Cell morphologyCytoskeletonFluorescence microscopyImage analysis

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Area of Science:

  • Cell Biology
  • Bioimaging
  • Computational Biology

Background:

  • Accurate cell segmentation is crucial for quantitative analysis of fluorescence microscopy images.
  • Deep learning models like Cellpose offer automated cell segmentation but can produce errors.
  • Training custom models requires programming expertise, limiting accessibility for wet lab researchers.

Purpose of the Study:

  • To develop an intuitive, code-free desktop application for quality control of automated cell segmentation.
  • To improve the accuracy and efficiency of single-cell analysis from fluorescence microscopy data.
  • To make advanced cell segmentation techniques more accessible to researchers without coding skills.

Main Methods:

  • Developed 'Toggle-Untoggle', a standalone desktop application for interactive cell segmentation quality control.
  • Integrated Cellpose models ('cyto3', 'nuclei', and custom models) into the application.
  • Implemented a user-friendly graphical interface for toggling, merging, and drawing cell masks.

Main Results:

  • Demonstrated the utility of Toggle-Untoggle for accurate and efficient single-cell analysis.
  • Enabled users to interactively refine automated cell segmentations without coding.
  • Facilitated the export of morphological features and cell outlines for downstream analysis.

Conclusions:

  • Toggle-Untoggle provides a valuable solution for code-free quality control of automated cell segmentation.
  • The application enhances the accessibility and efficiency of quantitative single-cell analysis in fluorescence microscopy.
  • This tool empowers wet lab researchers to perform accurate cell segmentation and analysis with ease.