<commit_before># High throughput detection and tracking of migrating neurons and neurites in live cell imaging


## About
Neuritetracker is software for high throughput detection, tracking, and segmentation of neuroblasts and neurites as they migrate in live cell imaging.

## Installation
To install neuritetracker on your machine follow these steps:

1. Obtain a licensed copy of Matlab.
2. Clone the **neuritetracker** repository using the following command line ```git clone <EMAIL>:sgbasel/neuritetracker.git``` or download a [zip file](https://github.com/sgbasel/neuritetracker/archive/master.zip) of the repository 
3. Set-up the **vlfeat library**. Run ```neuritetracker/vlfeat-0.9.18/toolbox/vl_setup.m``` at the Matlab prompt.
4. Compile the **Geodesics** functions. Run ```neuritetracker/Geodesics/compile_mex.m``` at the Matlab prompt.

## Running the code
Open Matlab and

1. trkTracking : to be run for one single sequence
2. processPlate.m
3. processListOfPlates.m

## Summary of the method
Details of the method are described in the article
<commit_msg>Changes to readme.<commit_after># High throughput detection and tracking of migrating neurons and neurites in live cell imaging


## About
Neuritetracker is software for high throughput detection, tracking, and segmentation of neuroblasts in live cell imaging.

## Installation
To install neuritetracker on your machine follow these steps:

1. Obtain a licensed copy of Matlab.
2. Clone the **neuritetracker** repository using the following command line ```git clone <EMAIL>:sgbasel/neuritetracker.git``` or download a [zip file](https://github.com/sgbasel/neuritetracker/archive/master.zip) of the repository 
3. Set-up the **vlfeat library**. Run ```neuritetracker/vlfeat-0.9.18/toolbox/vl_setup.m``` at the Matlab prompt.
4. Compile the **Geodesics** functions. Run ```neuritetracker/Geodesics/compile_mex.m``` at the Matlab prompt.

## Running the code
Open Matlab and

1. trkTracking : to be run for one single sequence
2. processPlate.m
3. processListOfPlates.m

## Summary of the method
Details of the method are described in the article

{'fraction_non_alphanumeric': 0.08561967833491012, 'fraction_numerical': 0.010406811731315043, 'mean_word_length': 4.957746478873239, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2380691', 'n_tokens_mistral': 629, 'n_tokens_neox': 611, 'n_words': 255}