This project is meant to analyze brain images based on cell shape features. The functions are:
- Extracting cells from brain images
- Learning cell shape features
- Training decision trees with cell shape features
- Generating detection score maps
- Finding statistically significant regions
- To be continued
Developed with Python 3.7.
Please read the Installation.md for the details of the installation process.
This step is to extract cells from brain section images and permute the generated cell patches in a random order.
Cell_extractor_local.md offers a guided example showing how to complete this step on your computer locally.
To speed up the process, you can refer to (Cell_extractor_aws.md) for the method to run on multiple AWS instances. Essential credential files of AWS and datajoint (VaultBrain in Installation.md) are required.
This step is to find representative cell patches via K-means++ and then use them to calculate diffusion map.
Diffusionmap.md provides a guided example showing how to complete this step on your computer.