search

cawarwick / Suite2p-Output-Processor

Process the stabilized outputs of Suite2p for manual ROI selection
1 stars 0 forks source link

Add montaging function for 3d data #4

Open cawarwick opened 2 years ago

cawarwick commented 2 years ago

Could be an option for expediting ROI generation

  1. Iterate the montage maker to make montages of matching chunks (e.g. the 2000 frames that Suite2p spits out)
  2. Now we have a 2x3 montage at 1x speed and we can run a multi-measure on the individual pieces so the ROIs match the 2x3 montage that would be used during ROI generation
  3. For depth alignment a rework in that function is overdue anyway, so maybe code in if>resolution in X, then it's P2 or whatever.
  4. Otherwise at least add montaging for 20x avgs
cawarwick commented 11 months ago

I started this on my pc, the V5 version has this partly implemented but it is not well tested.

cawarwick commented 11 months ago

V6 can montage the averages of 5 or 6 planes into a single file. The full montage is there but don't use because it'll be too big. My thoughts coming back to this are as follows:

  1. Neutral/Pro? Would it be nice to have a single file to open rather than check each one? Or is that the same amount of work since you can't look at each plane at the same time?
  2. Neutral? It's nice to see the activity in each plane at the same time, but how important is it for ease of use?
  3. PRO: Depth pipeline would certainly be faster, e.g. it would only require to be once since there is only 1 set of ROIs
  4. PRO: Multimeasure would need to be done as a script rather than manually, BUT would only need to be run once rather than having to open, save, and close 5 different times.
  5. Neutral. the output of the multimeasure would be huuuuge, like ~500mb, huge. Not ideal for ever opening. I suspect we'd need to interface with the csvs entirely through Python since I'm not sure excel could handle it, e.g. pulling traces we'd need to use a script to pull specific cells. (EDIT: I just tried this and it actually works pretty well. I merged all the csv into a single huge 500mb CSV and it opens and closes fine. Certainly longer than the individual CSVs but it was fine. The CSV format must just be easier for excel to manage)
  6. PRO: The cells would no longer have that stupid Exp_Plane_ROI and would just be a singular ROI name.
  7. CON: The suite2p processor would take even longer to run than it currently does.
  8. CON: I'd actually have to find the time to write the code