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magland / ml_ms4alg

MountainSort v4
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running `mountainsort` without `geom.csv` #39

Open marcoistasy opened 2 years ago

marcoistasy commented 2 years ago

Hello,

I am trying to sort data from Behnke Fried contacts. However, the exact or even approximate geometry of the contacts is unable to be determined. I am wondering if there is anyone to run this algorithm without using a geom.csv file.

I know that in the old (MATLAB) version of mountainsort there was an 'adjacency_radius' flag which could be set to 0 to sort each channel independently or to -1 to indicate that there is only one electrode neighborhood containing all the channels. I am wondering if this functionality is exposed in the new mountainsort algorithm using the MountainLab? That is, the one that is installed using

conda install -c flatiron -c conda-forge \
            mountainlab \
            mountainlab_pytools \
            ml_ephys \
            ml_ms3 \
            ml_ms4alg \
            ml_pyms

as per here.

magland commented 2 years ago

@marcoistasy I would recommend creating a geom.csv that has all the electrodes located at (0,0). Or make up a linear geometry. Then they will all be sorted together in one neighborhood.