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About
ecc is a small Python program to perform cell detection. It will identify the XYZ position, expression amount, and volume of the targeted cells from 3D mouse brain image. It essentially wraps around ilastik, a machine-learning framework to train pixel classifiers.
The detected cell table (given as csv format) can be further analyzed and visualized by using CUBIC-Cloud cloud computing service.
Table of contents
- Installation
- Workflow overview
- About Brain coordinates
- Data preparation
- Training ilastik classifier
- Applying ilastik classifier
- Segmenting objects