proudly presents socomap — the first easy-to-use online whole-brain segmentation service for automated detection of millions of neurons in 3D whole mouse brain datasets. Our pipeline achieves excellent accuracy and reduces the required human input by orders of magnitude, enabling high-throughput analysis. In order to get brain region specific cell counts the segmented datasets are mapped on to the Allen Brain Atlas.

For example, region specific c-Fos expression levels can easily be quantified from whole mouse-brain serial two-photon tomography stacks (fig. 1). A total of > 1.8 million somata were automatically segmented. Quality scoring yielded an F1-score of > 0.97 and a false merger rate < 5% for both, low and high density regions.

Just upload your dataset at, and we take it from there!

Learn more about how socomap is used in one of our case studies.

About us is a Swiss company dedicated to the annotation and segmentation of biological tissue and ultrastructures in 3D light and electron microscopy stacks.

We combine human and artificial intelligence to accelerate and facilitate innovation in life science. Our workflows integrate state-of-the-art deep learning algorithms, manual image annotation, and segmentation proofreading by human experts.

Leisibachstrasse 30
6033 Buchrain