Introducing socomap

A fully automated whole-brain segmentation platform

socomap is an online platform for analyzing whole-brain light microscopy stacks of mice. We provide highly accurate soma segmentation and cell counts for all cells expressing a specific marker in your dataset. We also offer brain region specific cell counts by mapping the dataset to the Allen Brain Atlas.

Visualization of soma segmentation, color-coded per region (scale bar represents 1.4 mm).

Cell Body/Soma Segmentation

  • Shape, location, and number of all cells in the dataset


Brain Region Mapping

to Allen Brain Atlas

  • Dataset mapping to the Allen Brain Atlas
  • Labeling of existing soma segmentation according to their brain region


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