CoLD: Cortical Layer Discrimination
This repository contains the Matlab code and example data associated to our manuscript Discrimination of the hierarchical structure of cortical layers in 2-photon microscopy data by combined unsupervised and supervised machine learning, published in Scientific Reports:
@article{Li2019,
author = {Li, Dong and Zavaglia, Melissa and Wang, Guangyu and Hu, Yi and Xie, Hong and Werner, Rene and Guan, Ji-Song and Hilgetag, Claus C.},
title = {Discrimination of the hierarchical structure of cortical layers in 2-photon microscopy data by combined unsupervised and supervised machine learning},
journal = {{S}cientific {R}eports},
year = {2018},
volume = {9},
number = {1},
pages = {7424},
doi = {10.1038/s41598-019-43432-y},
URL = {https://doi.org/10.1038/s41598-019-43432-y}
}
In case of usage of our code or data, we expect the above publication to be cited.
The code has been tested with Matlab R2017a on Windows 10.
The image data are further made available using git-lfs.
Before cloning the repository, please ensure that you installed git-lfs.
- Download the example data (see above link).
- Add subroutine folders (see below) to your Matlab environment.
- Run respective scripts.
- Send us a message in case of problems.
The folder ./discrimination contains the scripts to reproduce cortical layer. The main is script is the Discrimination_Main_Code.m file. The subfolder ./discrimination/subroutine_discrimination has to be integrated into the Matlab environment.
The folders ./evaluationclustering and ./evaluationsupervisedlearning contain the scripts to evaluate the unsupervised clustering and supervised learning results, respectively.
The folder ./exampledata contains example image data: the raw data and preprocessed data using the vignetting correction approach described here; cf. the corresponding github repository.