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Related Experiment Video

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Histological-Based Stainings Using Free-Floating Tissue Sections
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An automated mapping method for Nissl-stained mouse brain histologic sections.

Smadar Shiffman1, Sayantani Basak1, Cleopatra Kozlowski1

  • 1Safety Assessment Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA94080, USA.

Journal of Neuroscience Methods
|August 11, 2018
PubMed
Summary

Automated brain mapping accurately identifies neuroanatomic structures in mouse brain sections, reducing manual effort for neuropathologic assessments in research studies.

Keywords:
Automated image analysisBrain atlasBrain mapImage segmentationMouse histologic sections

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Area of Science:

  • Neuroscience
  • Computational Biology
  • Histology

Background:

  • Histologic evaluation of the central nervous system is crucial for in vivo efficacy and neurotoxicity studies.
  • Automated image analysis offers a solution to reduce the workload of evaluating brain histologic sections.

Purpose of the Study:

  • To develop an automated brain mapping method for identifying neuroanatomic structures in mouse brain sections.
  • To improve efficiency and consistency in neuropathologic assessments.

Main Methods:

  • Developed an automated method using the Allen Brain Atlas to map neuroanatomic structures on digitized Nissl-stained mouse brain sections.
  • Validated the method by comparing results to the Franklin and Paxinos (FP) mouse brain atlas and manually annotated sections.

Main Results:

  • The automated method accurately mapped brain regions and calculated volumes, comparable to manual delineations from the FP atlas.
  • Applied to in vivo study data, the method successfully mapped hippocampal boundaries for optical density quantification, yielding comparable results to manual methods.
  • Validation included comparison with a secondary atlas and manual annotations from 68 mice.

Conclusions:

  • The automated brain mapping method requires less manual input compared to existing techniques.
  • This method enhances efficiency and consistency in mouse neuropathologic assessments.