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Workflow Diagrams

This page provides additional visual representations and workflow details for the blech_clust pipeline.

Main Spike-Sorting Pipeline

For the complete spike-sorting pipeline workflow (including the operations workflow diagram, detailed steps, and nomnoml schema), please refer to the README.

Quality Assessment Workflow

blech_units_characteristics.py → blech_data_summary.py → grade_dataset.py

Additional Workflow Details

Spike Sorting Text Flow

[blech_exp_info] -> [blech_init]
[blech_init] -> [blech_common_average_reference]
[blech_common_average_reference] -> [bash blech_run_process.sh]
[bash blech_run_process.sh] -> [blech_post_process]
[blech_post_process] -> [blech_units_plot]
[blech_units_plot] -> [blech_make_arrays]
[blech_make_arrays] -> [bash blech_run_QA.sh]
[bash blech_run_QA.sh] -> [blech_units_characteristics]
[blech_units_characteristics] -> [blech_data_summary]
[blech_data_summary] -> [grade_dataset]

EMG Analysis Workflows

Shared Steps:

[blech_init] -> [blech_make_arrays]
[blech_make_arrays] -> [emg_filter]

BSA/STFT Branch:

[emg_filter] -> [emg_freq_setup]
[emg_freq_setup] -> [bash blech_emg_jetstream_parallel.sh (generated)]
[bash blech_emg_jetstream_parallel.sh] -> [emg_freq_post_process]
[emg_freq_post_process] -> [emg_freq_plot]

Note: emg_freq_setup.py generates the blech_emg_jetstream_parallel.sh script for parallel processing.

QDA Branch:

[emg_filter] -> [emg_freq_setup]
[emg_freq_setup] -> [gape_QDA_classifier/get_gapes_Li]

Using the Diagrams

Viewing the Workflow

The operations workflow visual (available in the README) provides a high-level overview of the entire pipeline, showing how different components interact.

Generating Custom Diagrams

  1. Visit nomnoml.com
  2. Copy the nomnoml schema code from the README
  3. Paste it into the editor
  4. Modify as needed for your specific use case
  5. Export as PNG or SVG

Understanding the Flow

  • Spike Sorting: The main pipeline processes raw Intan data through clustering and quality assessment
  • EMG Analysis: Two parallel branches for different analysis approaches
  • BSA/STFT: Frequency-based analysis using Bayesian methods
  • QDA: Gape detection using quadratic discriminant analysis

See Also