Matches

In the original version of track2p there are two types of output:

• A matrix (plane#_match_mat.npy) containing the indices of matched neurons across the session for a given plane (# is the index of the plane). Since matching is done from first day to last, some neurons will not be sucessfully tracked after one or a few days. In this case the matrix contains None values. To get neurons tracked across all days only take the rows of the matrices containing no None values.

• A track_ops.npy object that contains the parameters used for the algorithm and some intermediate results that can be used for visualisations (e. g. registered images and ROIs etc.)

Since the original plane#_match_mat.npy depends on the method used for filtering cells (e. g. ROIs are re-indexed depending on if the user chooses manual curation or different versions of iscell_threshold), we decided to add outputs that are agnostic to this (e. g. using the default suite2p indices before filtering depending on iscell.npy). Using this makes it much easier to load data. This output is saved as plane#_suite2p_indices.npy (and the equivalents in .mat and .csv formats).