hs13/mesoholo_onlineanalysis

All of the below are instructions for online analysis in the MesoSI computer

ONLINE ANALYSIS FOR MESOHOLO EXPERIEMENTS
crop the FOV down to the ActualHoloFOV in jupyter notebook, then run suite2p
open Anaconda Powershell Prompt and enter the following commands:
conda activate CLbehavior
cd to this folder jupyter notebook
in Matlab R2021b, run mesoscope_json_from_scanimage_210617_59.m
in jupyter notebook, run mesocroph5_justgreen.ipynb (took <15min total for HS_Ai203_2\220531\ : ~2min for conversion to h5,~12min for suite2p)
for full FOV, run mesofullh5parallels2p.ipynb (took 41min total for HS_Ai203_2\220531\ : ~3min for conversion to h5,~38min for suite2p))
to run both channels in cropped FOV, run mesocroph5s2p_allch.ipynb (haven't tested this code, might run into out-of-memory error depending on the recording length)

HOW TO FIND COORDINATES CORRESPONDING TO ActualHoloFOV BOUNDARIES IN YOUR CURRENT MROI SETTING
run the following in the MATLAB instance running Scanimage
find out ActualHoloFOV boundaries using convertcoords_HoloFOVtoCurrentFOV.m
the arguments for convertcoords_HoloFOVtoCurrentFOV should already be in the workspace if makeMasks3D_holeburn.m was run that day
xynew(:,1) is the horizontal axis, xynew(:,2) is the vertical axis
set xlb, xub (horizontal axis) and ylb, yub (vertical axis) accordingly in mesocroph5.ipynb
execute the following two lines in Matlab xyorig = [50 50; fullnpix_orig(1)-50 fullnpix_orig(2)-50];
xynew = convertcoords_HoloFOVtoCurrentFOV(hSI,xyorig, fullnpix_orig, fullxsize_orig, fullysize_orig, fullxcenter_orig, fullycenter_orig)

HOW TO INSTALL CLbehavior ENVIRONMENT
open Anaconda Powershell Prompt and enter the following commands:
cd C:\Users\MesoDAQ\Documents\GitHub\MesoSI_HScode\CLbehavior
conda env create -f environment.yml