Cell Segmentation and Tracking

By Nanyan "Rosalie" Zhu and Chen "Raphael" Liu, Columbia University, 2019

Please cite our paper if you find this useful.

Overview

The purpose of this repository is to design and implement a tool to quantify the cellular behaviors at the single-cell level. We decided to approach this challenge by dissecting it into two stages: cell segmentation and cell tracking. The quantification of cellular properties/behaviors is a natural outcome as the cell tracking stage is complete.

Repository Hierarchy

Cell_Segmentation_and_Tracking
    ├── Cell_Segmentation
    │   ├── Prediction_only
    │   │   └── Step01_raw_channels
    │   │   └── Step02_channel_combined_input
    │   │   └── deep_learning_model
    │   │   └── model_weights
    │   │   └── results
    │   │   └── Image_preprocessing.py
    │   │   └── Visualization.py
    │   │   └── misc_functions.py
    │   └── Train_n_Testing
    │       └── deep_learning_model
    │       └── ...
    └── Cell_Tracking
        └── ...

The Cell_Segmentation_and_Tracking repository contrains two folders, Cell_Segmentation and Cell_Tracking. These two folders are very much self-explanatory. Descriptions about their respective contents are described in the documentation files within each of them.

*Note 1: We did not include the "pycache" folders because they can be ignored practically.

*Note 2: We did not include the ".gitattribute" files and "README.md" files in the hierarchy tree. The former are utilized by the git large file storage (git-lfs) while the latter are the documentations, just like the one you are reading right now.