We believe that all science should be open-source. In this light, this Wiki page contains all the raw data and scripts to reproduce all the figures in our paper.
All analysis, including statistical analysis, were done in custom Python code. All raw data is stored in one of the following formats: .nex5, .tif, .hdf5, .csv. The code and raw data is available [here][1]. To download click "download as zip" and then decompress the zip folder.
In order to reproduce the figures you will need a python environment with the following packages installed:
- Caiman (for installation please see: [Caiman installation][2])
- Numpy
- Pandas
- Scikit-learn
- Scipy
- h5py
- Scikit-image
- Matplotlib
- Seaborn
- Statsmodels
- Tqdm
- Copy
- cupy (not essential, only for running the 2-photon analysis in the GPU. Requires a dedicated NVIDIA GPU)
Additionally, three more modules are needed for running the analyses (nexfile, all_functions, kl_classes2) but do not need to be installed, just downloaded.
To run the code make sure that you change the "path" variable on the first line of code, and then just hit run.
The code is commented, but if you have any questions or concerns please feel free to reach out at alegariamacal@wustl.edu
[1]: https://osf.io/8j7g2/files/
[2]: https://caiman.readthedocs.io/en/master/Installation.html