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ACCT is a fast and accessible automatic cell counting tool using machine learning for 2D image segmentation.

Theodore J Kataras1,2, Tyler J Jang1,2, Jeffrey Koury2

  • 1Graduate Program of Genetics, Genomics and Bioinformatics, University of California, Riverside, Riverside, CA, 92521, USA.

Scientific Reports
|May 22, 2023
PubMed
Summary

We developed Automatic Cell Counting with Trainable Weka Segmentation (ACCT), a novel tool for precise and accessible automatic cell counting in neuroscience research. ACCT offers a trainable solution to overcome the limitations of manual cell quantification.

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Area of Science:

  • Neuroscience
  • Cell Biology
  • Bioinformatics

Background:

  • Accurate cell counting is crucial for tracking disease progression in neuroscience.
  • Manual cell counting is time-consuming, difficult to standardize, and prone to error.
  • Existing automated tools lack sufficient accuracy and accessibility.

Purpose of the Study:

  • To introduce Automatic Cell Counting with Trainable Weka Segmentation (ACCT), a novel tool for automated cell quantification.
  • To demonstrate ACCT's flexibility and accuracy in cell counting through user-driven training and object segmentation.
  • To provide an accessible and precise automated solution for cell quantification in neuroscience research.

Main Methods:

  • Development of ACCT, a novel tool integrating Trainable Weka Segmentation for automatic cell counting.
  • Comparative analysis of ACCT against manual cell counts using publicly available neuron images and an in-house microglia dataset.
  • Validation of ACCT's performance without requiring high-performance computing or complex data preparation.

Main Results:

  • ACCT enables flexible automatic cell counting through user-guided segmentation.
  • The tool demonstrated accurate quantification of cells in both neuron and microglia image datasets.
  • ACCT provides a precise and accessible alternative to manual cell counting.

Conclusions:

  • ACCT offers a significant improvement for automated cell quantification in neuroscience.
  • The tool is accessible, requiring no specialized hardware or extensive data preparation.
  • ACCT facilitates precise and standardized cell counting, aiding in disease progression tracking.