daharoni/miniscope_analysis

MATLAB analysis functions for Miniscope project.

miniscope_analysis's Issues

general design issue

In general, you guys made a great work developing Miniscope hardware and firmware, but using Matlab for analysis makes it kind of partial solution. Some researchers will be forced to pay up to 10,000 USD for the Matlab license, depending on the country of usage. Moreover, msAutoSegment2() designed in a way that it loads the whole set of videos into memory, causing Matlab to crash on my 12Gb RAM PC. Unfortunately the typical case in the nowadays science is when a software developed in a Lab will work in that Lab only and abandoned after The Paper was published. Hope this project will avoid such fate.

msColumnCorrection, msReadFrame broken

msRun.m line: ms = msColumnCorrection(ms,5); %Generally not used
First of all "Generally not used" is misleading because de-facto many following function calls use result generated by msColumnCorrection().
msColumnCorrection.m is broken or not compatible with Matlab R2011b I'm using.
meanFrame = zeros(vidObj.height,vidObj.width); %allocate memory
The line above allocate 2D array (height x width), however,
msReadFrame(vidObj,frameNum,false,false,false) return 3D array (height x width x 3) causing this line to fail:
meanFrame = meanFrame + double(msReadFrame(vidObj,frameNum,false,false,false));

msExtractBehavoir() is not backward compatible with older Matlab versions

msExtractBehavoir.m line:
backgroundIndex = repmat(backgroundIndex,1,1,3);
In R2011b (and maybe in later releases) repmat does not support such calling syntax (cause "too many input arguments" error). Try guess why this new (and absolutely useless) repmat calling syntax was introduced in the new Matlab releases...

Please add a license.

https://choosealicense.com/no-license/
Absence of license file means no one else can use this code/software without being at risk of dealing with lawyers.
"If you find software that doesn’t have a license, that generally means you have no permission from the creators of the software to use, modify, or share the software. Although a code host such as GitHub may allow you to view and fork the code, this does not imply that you are permitted to use, modify, or share the software for any purpose."