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ransona / ROIMatchPub

Match suite2p ROIs between imaging sessions
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Interpreting the results: matching up ROI#s across days #1

Open sarahapark opened 3 years ago

sarahapark commented 3 years ago

Hello, I'm having trouble interpreting the results. The Ranson ROI#s and the Suite2p ROI#s are not matching up for me.

The instructions say: "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:

Does this mean, for example, if the cell ID number in roiMatchData.allSessionMapping = 2, then it is the index (= 2) of the 2nd Fall.iscell(:,1) = 1? So, the corresponding ROI # would be that of Fall.iscell(2,1) of only the true cells?

Or, does this mean, if the cell ID number in roiMatchData.allSessionMapping = 2, then it is the index (= 2) for the 2nd Fall.iscell(:,1) of both true and false cells?

Or, if the cell ID number in roiMatchData.allSessionMapping = 2, does this mean it is referring to the Suite2p ROI# = 2?

Thank you, Sarah

marysethomas commented 3 years ago

Hi Sarah, I have used this function before. It is the first case that you have laid out. You can check this by verifying that the number of true cells in your Fall.iscell is equal to roiMatchData.rois.cellCount. The numbers in allSessionMapping will never exceed the cell count, since they are an index and not the suite2p ROI number.

sarahapark commented 3 years ago

Hi Mary, Thanks so much for your feedback! The results make sense now! This is great!

Best regards, Sarah

marysethomas commented 3 years ago

No problem :)

sarahapark commented 3 years ago

Hi again, Does roiMatchData save the indices of all the ROIs that were initially detected pre-validation? If so, where can I find this data?

Thank you! Sarah

marysethomas commented 3 years ago

Hi Sarah, Just to make sure I understand your question, what do you mean by pre-validation?

sarahapark commented 3 years ago

Hi Mary, By "pre-validation", I mean all the longitudinal overlapping ROIs that are detected after pressing "Auto detect" and before going through the "Validate" step. For now, I've been going through the "Validate" step twice: the first time, I accept all ROIs and save the results. The second time, I accept only the "good" ROIs and save the results.

marysethomas commented 3 years ago

Ah okay, unfortunately I don't know about that! I hadn't noticed this feature.

sarahapark commented 3 years ago

Thank you anyways!

sarahapark commented 3 years ago

I have another question. What does the "compare pair" button do?