SpikeSorting: Object Space Task Pipeline

Automatic and manual spike sorting for tetrode recordings based on SpikeInterface.

Dependencies

Same as SpikeInterface

⚠️ Important: This pipeline uses the SpikeInterface version from 2020. Compatibility has not been tested with newer versions.

Please install each sorter as described here:
👉 SpikeInterface Sorter Installation Guide

If the method above causes issues, try these detailed installation instructions (PDF).

When using Matlab-based sorters, save them in:

~/Documents/SpikeSorting/

To be used on Linux 🐧. Add this folder to your path temporarily:

export PYTHONPATH=$PYTHONPATH:/path/to/this/folder

To make it permanent, paste it into your bashrc:

gedit ~/.bashrc

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Spike Sorting Pipeline

1. Activate your conda environment

conda activate <Name of environment>

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2. Check for corrupt or uneven length files

python -m check_length ‘/full/path/to/folder_with_Study_day_subfolders’

⚠️ Ensure trial folders don’t have duplicate channel files like 100_CH1.continuous and 100_CH1_2.continuous.

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3. Select trials or merge trials (Trial1 + PostTrial1 or full-day)

Use merge_channels_revised_T1_PT1.m or merge_channels_revised.m in MATLAB.
Ensure correct sampling rate (fs):

• Rats 1–9 used 20kHz, not 30kHz.

Check folders variable in the MATLAB script and make sure it lists the correct trial folders in the right order.

📌 Refer to the file:
RAT_OS_EPHYS_Channel_Normalization_Across_Animals.xlsx (Dropbox)

💡 Run merging twice:

1. Trial1 + PostTrial1
2. Presleep + T1 + PT1 + … + T5 + PT5 (+ Novelty trial if applicable)

📋 Refer to this Google Planning Sheet

Generate hpc.xlsx and cortex.xlsx with tetrode IDs and channel info.
Skip tetrodes with only 1 channel or reference tetrodes.

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4. Fix file names if needed

python -m fix_channel_name ‘/path/to/continuous_files’

Copy the following files from the same study day (any trial or post-trial folder):

• all_channels.events
• Continuous_Data.openephys
• messages.events
• settings.xml
• tetrode.prb (same for all rats)
• hpc.xlsx and cortex.xlsx (omit hpc.xlsx if not sorting HPC)

💻 Work locally! Copy the merged folder to your computer's data hard drive.

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5. Rearrange data by tetrode

python -m rearrange_folders ‘/path/to/merged_data’

📌 If only sorting cortical tetrodes, ensure rearrange_folders.py uses:

folders = ['cortex']

Instead of:

folders = ['hpc', 'cortex']

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6. Run automatic spike sorting

python -m run_tetrodes ‘/path/to/brain_region_folder_with_tetrodes’

💡 Prefer using Spyder (prevents crashes):

conda activate spiketutorial
spyder

In Spyder:

• Load run_tetrodes.py
• Set the correct path in the folder variable
• Press Ctrl+A then F9 to run the script

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7. Create JSON for consensus

python -m create_json ‘/path/to/brain_region_folder’

Copy JSON files to the respective brain area folders of the full-day merged folder.

To run manual curation:

python -m run_tetrodes_manual ‘/path/to/brain_region_folder_with_tetrodes’

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8. Manual curation with Phy

During manual curation:

• Alt+N = Noise
• Alt+M = MUA
• Alt+G = Pyramidal unit
• Leave unlabeled = Interneuron

⚠️ Always save first, then close. If you close first and then save, your curation won't be saved.

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9. Activation matrix & consensus post-curation

Both scripts (run_tetrodes.py or run_tetrodes_manual.py) create a phy folder with:

• spike_times.npy
• spike_clusters.npy

You can generate activation matrices (25 ms bins) as actmat_auto_tetrode#.

To concatenate and detect assemblies:

python -m phy2assembly

To view previous detections:

os.system('phy template-gui phy_AGR/params.py')

Post-curation consensus:

python -m consensus_post_curation ‘/path/to/tetrode_folder’

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10. Quality Metrics

python -m quality_metrics

Requires:

conda env create -f environment_qm.yml
conda activate spiketutorial_qm

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Running in Spyder

1. Open run_tetrodes.py
2. Press Ctrl+A, then F9

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Running in Linux Terminal (Adrian's PC only)

./loop

This calls run_tetrodes_brain_areas.py in a loop.
Download loop.sh → rename to loop.

Add loop to your PATH in ~/.bashrc.

Modify sorter.py: add exit() to the end of ms4() and auto() functions.

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Reading corrupted Open Ephys files

Navigate to:

/home/Username/anaconda3/envs/spiketutorial/lib/python3.6/site-packages/pyopenephys

Modify:

• openephys_tools.py
• core.py

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Newest scripts (yet to be described)

• run_tetrodes_brain_areas.py
• run_tetrodes_json.py
• run_tetrodes_loop.py
• truncate2.py