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Related Experiment Video

Updated: Dec 30, 2025

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells
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3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images.

Ervin A Tasnadi1, Timea Toth1, Maria Kovacs1

  • 1Synthetic and System Biology Unit, Biological Research Centre (BRC), Szeged H-6726, Hungary.

Bioinformatics (Oxford, England)
|January 18, 2020
PubMed
Summary
This summary is machine-generated.

3D-Cell-Annotator offers semi-automated 3D cell segmentation for microscopy images. This computational biology tool achieves human-expert precision in segmenting complex biological structures like organoids.

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Area of Science:

  • Computational biology
  • Bioimage analysis
  • 3D imaging

Background:

  • Accurate single-cell segmentation in 3D microscopy is crucial for bioimage analysis and deep learning.
  • Existing methods face challenges in segmenting complex biological structures.

Purpose of the Study:

  • To introduce 3D-Cell-Annotator, a novel software for semi-automated 3D cell segmentation.
  • To leverage 3D active surfaces and shape descriptors for enhanced segmentation accuracy.

Main Methods:

  • Utilized 3D active surfaces and shape descriptors as prior information.
  • Integrated into the Medical Imaging Interaction Toolkit (MITK) via a CUDA/C++ patch.
  • Developed a semi-automated approach for user interaction.

Main Results:

  • Achieved segmentation precision comparable to human experts on 3D biological structures (spheroids, organoids, embryos).
  • Demonstrated effective segmentation using a user-friendly 3D interface.

Conclusions:

  • 3D-Cell-Annotator provides a powerful and accurate solution for 3D cell segmentation.
  • The software is accessible on Windows and Linux, requiring a CUDA-enabled GPU.