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Mesoscale microscopy and image analysis tools for understanding the brain.

Adam L Tyson1, Troy W Margrie1

  • 1Sainsbury Wellcome Centre, University College London, 25 Howland Street, London, W1T 4JG, United Kingdom.

Progress in Biophysics and Molecular Biology
|July 3, 2021
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Summary

New whole-brain microscopy generates complex data. This review covers open-source tools for analyzing mouse brain images, aiding neuroscience research and tool development.

Keywords:
Image registrationNeuroscienceSegmentationVisualisationwhole Brain microscopy

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Area of Science:

  • Neuroscience
  • Bioimaging
  • Computational Biology

Background:

  • Recent advances in whole-brain microscopy enable high-resolution imaging of intact small animal brains.
  • These complex datasets offer significant insights but pose computational challenges for many neuroscience labs.
  • Lack of accessible computational tools hinders the full utilization of whole-brain microscopy data.

Purpose of the Study:

  • To review current open-source computational tools for whole-brain microscopy data analysis.
  • To address the need for accessible tools in neuroscience laboratories.
  • To propose a collaborative pathway for developing integrated analysis pipelines.

Main Methods:

  • Literature review of open-source software for image registration, segmentation, visualization, and analysis.
  • Focus on tools applicable to high-resolution whole-brain images of model organisms like mice.
  • Identification of gaps in current analysis pipelines.

Main Results:

  • Several open-source tools are available for specific tasks like image registration to atlases and segmentation of brain regions and neuronal structures.
  • The field currently lacks comprehensive, integrated analysis pipelines for all whole-brain microscopy data types.
  • Existing tools vary in accessibility and integration capabilities.

Conclusions:

  • Open-source tools are crucial for advancing whole-brain microscopy data analysis in neuroscience.
  • Collaboration between tool developers is essential to create integrated pipelines.
  • A coordinated effort can overcome computational barriers and unlock the full potential of whole-brain imaging.