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HC-6 ca1/ca3 storage pattern

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HC-6 ca1/ca3 storage pattern

Posted by Keiland Cooper at March 02. 2017

Is there a pattern of how the data is saved per tetrode to know which is ca1 and which is ca3? The documents don't seem to name a pattern aside from looking up each one. They seem to be randomly saved. If not, any links to Matlab software that can parse each of these? 

Hopefully, I am not overlooking a simple detail. 

Re: HC-6 ca1/ca3 storage pattern

Posted by Loren Frank at March 05. 2017

There is no pattern, as the numbering has to do with microdrive construction, which maps only indirectly onto which tetrode was targeted to each area.  It should be fairly straight forward to write a simple function that runs through the relevant day of the cellinfo structure to pull out the indices corresponding to the locations.  We have software for this, of course, but it's built into a somewhat complex analysis framework, so sending you the function wouldn't help much, I'm afraid.  

For reference, a function in matlab that gave you a complete list of cell indices would be something like this (with likely the need for more error checking)

location = 'CA1'

ca1list = [];

for d = 1:length(cellinfo)

    for e  = 1:length(cellinfo{d})

        for t = 1:length(cellinfo{d}{e})

            for c = 1:length(cellinfo{d}{e}{t})

            if ~isempty(cellinfo{d}{e}{t}{c}) && strcmp(cellinfo{d}{e}{t}{c}.location, location)

                ca1list = [ca1list ; d e t c];





This sort of search is why we organized the data the way we did; it makes it relativley easy to pull out whichever subsets of days, epochs tetrodes or cells you're interested in for a particular analysis.


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