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.

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Main Features

socomap is an automatic segmentation pipeline for whole-brain cell images

Soma Segmentation and Region Mapping

We offer segmentation of individual cells as well as a complete mapping of the dataset to the 71 regions defined in the Allen Brain Atlas and a labeling of each cell according to its region.

Automated Results

You simply submit your dataset into our pipeline, and get notified by results via e-mail. All results are also accessible from your account in our socomap dashboard.

Secure Upload and Storage

All uploads are encrypted, and get securely stored and backed up on storage servers located in the EU.

Highest Scientific Standards

We commit ourselves to delivering high-quality results by combining latest machine-learning research with in-house proofreading by our QA team, all holding Master degrees in Biology.

Simply upload your dataset into our segmentation pipeline

To use socomap, sign up for an account at our Dashboard. You can then upload datasets (up to 100 GiB), and submit them to our pipeline by selecting what kind of segmentation you want to order. We will then proceed with the analysis, and notify you by e-mail when results are available to download.

socomap Workflow

For datasets larger than 100 GiB, please contact us via e-mail, and we will manage your dataset accordingly.


We currently offer 2 segmentation options on light microscopy datasets. If these options don’t fit your dataset or if you are looking for different services, please get in touch with us.

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


Prices are displayed excluding VAT. VAT applies if your billing address is in Switzerland.