gitter-badger/cellfinder

Automated 3D cell detection and registration of whole-brain images

Cellfinder

Whole-brain cell detection, registration and analysis.

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Cellfinder is a collection of tools from the Margrie Lab and others at the Sainsbury Wellcome Centre for the analysis of whole-brain imaging data such as serial-section imaging and lightsheet imaging in cleared tissue.

The aim is to provide a single solution for:

• Cell detection (initial cell candidate detection and refinement using deep learning.
• Atlas registration (using amap)
• Analysis of cell positions in a common space

Installation is with pip install cellfinder, but full documentation can be found here.

This software is at a very early stage, and was written with our data in mind. Over time we hope to support other data types/formats. If you have any questions or issues, please get in touch by email or by raising an issue.

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Examples

more to come

Tracing of inputs to retrosplenial cortex (RSP)

Input cell somas detected by cellfinder, aligned to the Allen Reference Atlas, and visualised in brainrender along with RSP.

Data courtesy of Sepiedeh Keshavarzi and Chryssanthi Tsitoura. Details here