Joystick

The repository contains both an older joystick analysis stack and a newer reorganization:

  • joystick_basic_202304/
  • JoystickProcessing2026/

joystick_basic_202304/

This is the older, report-oriented joystick project.

Main components:

  • modules/: Trialization.py, Alignment.py, ReadResults.py, StatTest.py
  • plot/: field-of-view, perception, motor-alignment, model, raw-trace, and behavior figures
  • visualization_VIPG8.py, visualization_VIPTD_G8.py, visualization_L7G8.py: subject or cohort-specific report builders

The update notes in README.md show that this stack supports:

  • significance testing
  • ROI plots
  • short versus long block comparisons
  • outcome discrimination
  • block and transient decoding
  • joystick trajectory analyses
  • pooled session summaries

This project follows the same general pattern seen elsewhere in the repo:

  1. read processed imaging outputs
  2. trialize and align the session
  3. compute significance labels
  4. generate experiment-specific figure panels

JoystickProcessing2026/

This newer directory is split by pipeline stage rather than by one monolithic analysis script.

Subdirectories:

  • SessionsTrialization/: session-level trialization
  • InitialPlotting/: early analysis and plotting scripts
  • PostProcessing/: later postprocessing, spike-analysis summaries, and tau-selection utilities

Representative entry points include:

  • JoystickProcessing2026/SessionsTrialization/main.py
  • JoystickProcessing2026/InitialPlotting/main.py
  • JoystickProcessing2026/InitialPlotting/main_laptop.py
  • JoystickProcessing2026/PostProcessing/main.py
  • JoystickProcessing2026/PostProcessing/run_postprocess.py
  • JoystickProcessing2026/PostProcessing/run_manual_postprocess.py

This separation suggests a gradual migration away from the older one-directory project style toward more explicit stages.

Shared assumptions

Both joystick stacks assume upstream data from the common preprocessing and postprocessing layers, especially:

  • ops.npy
  • motion-correction outputs
  • ROI masks and labels
  • dff.h5
  • voltage recordings and Bpod metadata

Practical use

Use joystick_basic_202304/ if you need the established figure-generation code for existing joystick experiments.

Use JoystickProcessing2026/ if you are working with the newer reorganized workflow and want the staged scripts for trialization, initial plotting, and postprocessing.