yguo29/locanmf-preprocess

Preprocessing (denoising and atlas registration) functions for LocaNMF

LocaNMF-preprocess

Preprocesses calcium imaging data, eg. widefield calcium imaging, to use with LocaNMF. Read more about LocaNMF and the results it provides in our bioRxiv : Saxena et al., 2019!

Preprocessing instructions:

1. Save your data as a .mat file with calcium imaging video as variable 'Y', with dimensions: pixels x pixels x time.

2. Find an atlas of regions that segments the field of view into separate regions. For widefield calcium imaging data in the mouse dorsal cortex, use 'atlas.mat' provided in 'utils', which is based off of the Allen atlas, as in Musall et al., 2019.

3. Run process_dataset.m in MATLAB to:

   (a) define a brainmask

   (b) denoise the dataset

   (c) align / register the atlas to the dataset

4. Run LocaNMF!