Stable open field and VR

We implemented additional spatial analyses for open field and virtual reality data and added Continuous Integration.

Re-implemented matlab post-processing

Most of the matlab post-sorting processors are reimplemented. This is a working open field analysis version before rewriting the pre-processor to be able to use multiple spike sorters.

This version is able to run the pre-processing on separate tetrodes.

Working version before rewriting post-processing

A parallel python version will be developed to replace post-processing in MATLAB

Working version before major refactoring of postclustering script

extra plot for second series of stimulation

high freq stimulation has to be the last one - better method it needed to separate plots, such as another ttl pulse sent to open ephys

Sorting with MountainSort using continuous data - linux

This version is designed to run on a linux sorting computer. The main script monitors a designated folder (nolanlab/to_sort/recordings) on the computer, and calls all processing scripts if users put recordings in this folder (and added a copied.txt file as well to indicate that copying is complete).

Another option is to add a text file with a list of folders on the server that the script will copy when the 'priority' sorting folder is empty.
SpikeSortingPipeline.pptx

(1) OpenEphys continuous files are converted to mda format (in Python) both tetrode by tetrode (4 files) and all 16 channels together into one mda file. The folder structure required by MountainSort (MS) is created in this step, dead channels are removed.
(2) MountainSort (MS) is called (via a shell script written by the previous Python step) to perform spike sorting in the mda files, and saves the results in the local folder
(3) Matlab is called and port-processing is done. This makes plots of firing fields, light stimulation plots depending on the data, and saves the output on the lab's server based on a parameter file that's saved by the user in the original recording folder.

Spike sorting with mountainsort from spike data

Created folder structure from spike data for mountainsort, and organizes files for sorting.