By Nanyan "Rosalie" Zhu and Chen "Raphael" Liu, Columbia University, 2019
Please cite our paper if you find this useful.
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.
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.