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
15. The cell #s in roiMatchData.allSessionMappingPyIndex refer to the Suite2p ROI#s using python indexing (first index = 0).
16. The cell #s in roiMatchData.allAutoDetectedCellsPyIndex refer to the Suite2p ROI#s using python indexing (first index = 0) of ALL the cells auto detected before validation.