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Related Experiment Video

Updated: Jun 17, 2025

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AnNoBrainer, An Automated Annotation of Mouse Brain Images using Deep Learning.

Roman Peter1, Petr Hrobar2, Josef Navratil3

  • 1Discovery Informatics, MSD Czech Republic s.r.o., Na Valentince 4, FIVE Building, Prague 5 - Smichov, Prague, 150 00, Czech Republic.

Neuroinformatics
|August 6, 2024
PubMed
Summary
This summary is machine-generated.

An open-source tool, AnNoBrainer, automates mouse brain region annotation in digital pathology. This deep learning approach significantly reduces annotation time and increases reproducibility for high-throughput neuroscience research.

Keywords:
Deep learningImage registrationMouse brain

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Area of Science:

  • Neuroscience digital pathology
  • Computational pathology
  • Image analysis

Background:

  • Manual annotation of mouse brain regions is crucial but time-consuming and requires expert knowledge.
  • Current manual methods limit throughput in neuroscience digital pathology labs.
  • There is a growing demand for efficient image analysis in pharmaceutical research.

Purpose of the Study:

  • To develop an open-source software tool for automated annotation of mouse brain regions.
  • To improve the speed, accuracy, and reproducibility of brain image analysis.
  • To support high-throughput workflows in digital pathology.

Main Methods:

  • Developed AnNoBrainer, an open-source tool utilizing deep learning, image registration, and brain templates.
  • Applied AnNoBrainer to 2D pathology slides from transgenic mice models of synucleinopathy.
  • Compared automated annotation results with manual annotation by trained scientists.

Main Results:

  • AnNoBrainer achieved comparable accuracy to manual annotation.
  • The tool demonstrated increased reproducibility in brain region annotation.
  • AnNoBrainer reduced annotation time by approximately 50% compared to trained scientists.
  • Automated annotation met expert histopathological assessment standards in over 85% of cases.

Conclusions:

  • AnNoBrainer provides a rapid, accurate, and reproducible method for automated mouse brain image annotation.
  • The software enables efficient, high-throughput image analysis workflows in digital pathology.
  • AnNoBrainer largely meets expert standards, facilitating research in neuroscience and pharmaceutical settings.