Journal: Bioelectronic Medicine

Article Title: Framework for automated sorting of neural spikes from Neuralynx-acquired tetrode recordings in freely-moving mice

doi: 10.1186/s42234-021-00079-3

Figure Lengend Snippet: Overview of data analysis procedure. a, Automated spike sorting using MountainSort. Continuously sampled signals are collected in Cheetah, prepared for the MountainSort pipeline in MATLAB, sorted in MountainSort, and finally passed through MATLAB again prior to final analysis. b, Manual spike sorting using Spike2. Discrete spike channels are imported into Spike2, where all preprocessing takes place. Exported spikes are used for final analysis

Article Snippet: We have efficiently integrated the MountainSort spike sorter with Neuralynx-acquired neural recordings.

Techniques:

Journal: Bioelectronic Medicine

Article Title: Framework for automated sorting of neural spikes from Neuralynx-acquired tetrode recordings in freely-moving mice

doi: 10.1186/s42234-021-00079-3

Figure Lengend Snippet: Merging and converting data prior to automated spike sorting. a, Organization and preparation of data for MountainSort pipeline. Sessions from the same mouse on the same day are placed into the same folder, with the data files organized in each session folder just as they are saved by Cheetah. The parent folder containing all of the ‘mouse & day’ subfolders is input into MATLAB to merge and convert the data. The output files are organized by tetrode, and saved in the mouse & day folder as they contain the signals acquired for all sessions within the folder. b, The m2021_mergeandconvert.m script imports the CSC.ncs files and saves the merged data as raw.mda. Three other files are saved; params.json contains the sample rate and spike direction, geom.csv indicates the tetrode geometry, and t_info.csv contains the start and end times of each recording that are used to split the merged files for session-by-session analysis. The lower panel depicts the m2021_mergeandconvert.m script to be run

Article Snippet: We have efficiently integrated the MountainSort spike sorter with Neuralynx-acquired neural recordings.

Techniques:

Journal: Bioelectronic Medicine

Article Title: Framework for automated sorting of neural spikes from Neuralynx-acquired tetrode recordings in freely-moving mice

doi: 10.1186/s42234-021-00079-3

Figure Lengend Snippet: Automated sorting framework. a, The files raw.mda, params.json, and geom.csv are imported into the MountainSort pipeline, which includes both pre-processing and spike sorting. The MountainSort pipeline outputs firings.mda files, which contain the unit IDs and timestamps of sorted spikes. The designated input and output folders are entered into the runsort.sh script, as depicted in the bottom of the panel. b, Using the m2021_ms_out_timestamps.m script, sorted files are split back up into the original recording sessions according to the t_info.csv file. Split files are saved as spiketimes.txt, for easy transfer to other software package for final analysis. The m2021_ms_out_timestamps.m script is shown in the bottom of the panel. c, Output spiketimes.txt files are formatted as two columns of unit ID, timestamp pairs

Article Snippet: We have efficiently integrated the MountainSort spike sorter with Neuralynx-acquired neural recordings.

Techniques: Software

Journal: Journal of Neuroscience Research

Article Title: Trigeminal neuropathy causes hypomyelination in the anterior cingulate cortex, disrupts the synchrony of neural circuitry, and impairs decision‐making in male rats

doi: 10.1002/jnr.24903

Figure Lengend Snippet: Research resource identifiers of reagents and software used for experiments and analysis

Article Snippet: Single unit spike sorting was done using Offline Spike Sorter software (Version 4, Plexon Inc.).

Techniques: Software, Bicinchoninic Acid Protein Assay