Cell Proposal Network (CPN)

1. Introduction
2. Requirements
3. Instructions

Introduction:

This repository contains code for proposing candidate masks for biological cells in microscopy images. These cell candidates are used for cell tracking. The paper can be found at arXiv and tracking code is available at: Cell Tracker

If you find this code useful in your research, please cite:

@article{akram2017a,
    author = {Akram S. U., Kannala J., Eklund L., and Heikkilä J.},
    title = {Cell Tracking via Proposal Generation and Selection},
    journal = {arXiv:1705.03386},
    year = {2017}
}

This code is based on Faster R-CNN and many functions from original code were either used directly or with slight modifications. The code has many half finished and broken features, which i plan to either remove or fix in future. The code was re-structred recently and it may have introduced some bugs, which you may report (especially if they are in parts which are executed) and I will try to fix them. If and when I fix this code, I may remove the experimental exp branch.

Requirements:

1. CPN: Cell Proposal Network code.
   git clone https://github.com/SaadUllahAkram/CPN.git
2. caffe: Faster R-CNN version with crop layer.
   git clone https://github.com/SaadUllahAkram/caffe_cpn.git
3. BIA: a collection of useful functions.
   git clone https://github.com/SaadUllahAkram/BIA.git
4. MATLAB
   

Instructions:

1. Set Caffe, ISBI CTC data paths in get_paths.m function in BIA:
2. activate caffe using: bia.caffe.activate('cpn', gpu_id);

Testing (will be added soon)

1. run demo_test_cpn()

Training

1. Download Cell Tracking Challenge data.
2. run demo_train_cpn()