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DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection.

Rishi Koneru1, Manjari Anant2,3,4, Hyopil Kim1

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Summary

This study introduces DART, an open-source software pipeline for precise brain region dissection. DART aligns tissue sections to atlases, automating region identification for reproducible molecular analyses.

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Area of Science:

  • Neurobiology
  • Bioinformatics
  • Computational Neuroscience

Background:

  • Precise dissection of brain regions is crucial for neurobiology research.
  • Manual dissection and visual inspection are time-consuming and prone to error.
  • Laser capture microscopy improves accuracy but region identification remains a challenge.

Purpose of the Study:

  • To present DART (Dissecting Atlas-Registered Tissue), an open-source software pipeline.
  • To automate the identification and contouring of brain regions of interest (ROIs) for laser microdissection.
  • To enhance reproducibility and precision in tissue sampling for molecular analyses.

Main Methods:

  • DART aligns histological brain sections to 3D reference atlases.
  • It utilizes established image-processing libraries and a GUI.
  • The software exports ROI contours for Leica Laser Microdissection (LMD) instruments.

Main Results:

  • DART automates the historically laborious process of defining brain region boundaries.
  • The pipeline streamlines tissue sampling for molecular studies.
  • It ensures high precision and reproducibility in ROI selection.

Conclusions:

  • DART offers a significant advancement in automating brain region dissection for neurobiological research.
  • The software enhances the efficiency and accuracy of tissue sampling.
  • Researchers can achieve more reliable and reproducible results in molecular analyses.