blech_clust

Python and R based code for clustering and sorting electrophysiology data recorded using the Intan RHD2132 chips. Originally written for cortical multi-electrode recordings in Don Katz's lab at Brandeis. Optimized for the High performance computing cluster at Brandeis (https://kb.brandeis.edu/display/SCI/High+Performance+Computing+Cluster) but can be easily modified to work in any parallel environment. Visit the Katz lab website at https://sites.google.com/a/brandeis.edu/katzlab/

Order of operations

1. python blech_exp_info.py

   • Pre-clustering step. Annotate recorded channels and save experimental parameters
   • Takes template for info and electrode layout as argument

2. python blech_clust.py

   • Setup directories and define clustering parameters

3. python blech_common_avg_reference.py

   • Perform common average referencing to remove large artifacts

4. bash blech_run_process.sh

   • Embarrasingly parallel spike extraction and clustering

5. python blech_post_process.py

   • Add selected units to HDF5 file for further processing

6. python blech_units_similarity.py

   • Check for collisions of spiketimes to assess double-counting of waveforms in clustering

7. python blech_units_plot.py

   • Plot waveforms of selected spikes

8. python blech_make_arrays.py

   • Generate spike-train arrays

9. python blech_make_psth.py

   • Plots PSTHs and rasters for all selected units

10. python blech_palatability_identity_setup.py

11. python blech_overlay_psth.py

    • Plot overlayed PSTHs for units with respective waveforms

Setup

cd <path_to_blech_clust>/requirements               # Move into blech_clust folder with requirements files
conda clean --all                                   # Removes unused packages and caches
conda create --name blech_clust python=3.8.13       # Create "blech_clust" environment with conda requirements
conda activate blech_clust                          # Activate blech_clust environment
bash conda_requirements_base.sh                     # Install main packages using conda/mamba
bash install_gnu_parallel.sh                        # Install GNU Parallel
pip install -r pip_requirements_base.txt            # Install pip requirements (not covered by conda)

• Parameter files will need to be setup according to Setting up params

Convenience scripts

• blech_clust_pre.sh : Runs steps 2-5
• blech_clust_post.sh : Runs steps 7-14

Operations Workflow Visual

Example workflow

DIR=/path/to/raw/data/files  
python blech_exp_info.py $DIR  # Generate metadata and electrode layout  
bash blech_clust_pre.sh $DIR   # Perform steps up to spike extraction and UMAP  
python blech_post_process.py   # Add sorted units to HDF5 (CLI or .CSV as input)  
bash blech_clust_post.sh       # Perform steps up to PSTH generation

Test Dataset

We are grateful to Brandeis University Google Filestream for hosting this dataset
Data to test workflow available at:
https://drive.google.com/drive/folders/1ne5SNU3Vxf74tbbWvOYbYOE1mSBkJ3u3?usp=sharing