README.md

# Global Cell Linking

Project to provide Global linking of cell detections.
It is currently connected with an EmbedTrack segmentation routine.


***

## Prerequisities

- conda ![link](https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
- Gurobi Optimizer ![link](https://www.gurobi.com/downloads/gurobi-software/)

## Instalation


Clone the repository and update all its submodules. These are EmbedTrack an LibCT.


``` bash
git clone https://gitlab.fi.muni.cz/xlux/global-linking.git
cd global-linking
git submodule update --init --recursive

```

Then, create the conda evironment.

```bash
conda env create -f GlobalTracking.env
conda activate GlobalTracking
```


Load dataset CTC `BF-C2DL-HSC` to directory `DATA`.  
The final structure should should be following:

```
# Structure of training data directory
--DATA
    -- 'SUBSET'                             # Subset is 'train' or 'challenge'
        -- 'DATASET_NAME'                   # Name of dataset e.g. 'BF-C2DL-HSC
            -- 01                           # YY - name of sequence, a two digit number, e.g. '01', '02'
                -- t0000.tif
                -- t0001.tif
                ...
            -- 01_GT                        # GT, 'train' subset only
                -- SEG                      # segmentation reference
                    -- man_seg0000.tif
                    -- man_seg0001.tif
                    ...
                -- TRA                      # tracking reference
                    -- man_track.txt
                    -- man_track0000.tif
                    -- man_track0001.tif
                      ...
```

Open the notebook

``` bash
./run_notebook.sh
```


## Description
The project adds global linking to the existing EmbedTrack method.
It is tested on a data from Cell Tracking Challenge (http://celltrackingchallenge.net/).

## Authors and Acknowledgment
Filip Lux

I hereby thank to Katharina Loffler for providing me a guidance through EmbedTrack method.

## License
MIT License

Copyright (c) 2023 Filip Lux

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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