RoiMatchHelp.m

% 1) Start a new match file with the 'New match file' button
% 2) Click "Add experiment" to load the Fall.mat file output by suite2p.
% This will be the experiment that all others will be aligned to.
% 3) Click "Add experiment" to load the Fall.mat file from another
% experiment which you expect to have the same cells in it.
% 4) When the control point selection tool opens click some matching cells
% or other landmarks in the left (baseline experiment) and right
% (experiment you are adding) windows.
% 5) Once you've clicked cells/landmarks which cover the whole field of
% view close the control point selection tool.
% 6) You'll then see a comparison of the rois from the 2 sessions.
% 7) Repeat steps 3 - 5 to add all experiments where you want to
% longitudinally track cells.
% 8) Set the ROI overlap threshold and click 'Auto detect' to find
% potential matches over all experiments.
% 9) Click 'Show all' to show putative matches over all sessions.
% 10) Click validate and follow instructions in figure window to confirm
% cell by cell that the cells which have been matched over the sessions
% look the same as each other. 'ROI surround pixels' sets how much of the
% field of view surrounding the roi is show to help check it is the same
% cell.
% 11) Click 'Show valid' to show all of the cells you have visually
% inspected.
% 12) Click 'Save match file' to save what you have done. The saved file
% can be reloaded to work more on,
% 13) The same file an be loaded into matlab and has a field
% 'roiMatchData.allSessionMapping' which contains a matrix where rows are
% longitudinally identified cells and columns are sessions/separate
% experiments. 
% 14) The cell ID numbers in roiMatchData.allSessionMapping refer to the
% cells output by suite2p which have been classified as valid in the
% suite2p gui (found in Fall.iscell). i.e. cell ID number 8 in
% roiMatchData.allSessionMapping is the 8th valid cell output by suite2p