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https://github.com/chenliu-1996/cell_segmentation_and_tracking

For cell segmentation and tracking.

https://github.com/chenliu-1996/cell_segmentation_and_tracking

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    DOI references
  • ✓
    Academic publication links
    Links to: arxiv.org
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    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

For cell segmentation and tracking.

Basic Info
  • Host: GitHub
  • Owner: ChenLiu-1996
  • Default Branch: master
  • Homepage:
  • Size: 214 MB
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  • Stars: 2
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Fork of SAIL-GuoLab/Cell_Segmentation_and_Tracking
Created almost 5 years ago · Last pushed over 6 years ago

https://github.com/ChenLiu-1996/Cell_Segmentation_and_Tracking/blob/master/ 

# Cell Segmentation and Tracking
*By Nanyan "Rosalie" Zhu and Chen "Raphael" Liu, Columbia University, 2019*

#### Please cite [our paper](https://arxiv.org/pdf/2001.05548.pdf) 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.

Owner

  • Name: Chen Liu
  • Login: ChenLiu-1996
  • Kind: user
  • Location: New Haven
  • Company: Yale University

CS PhD student at @KrishnaswamyLab, @YaleUniversity. Reviewing Committee member at NeurIPS, ICLR, ICML.

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