omniroute_analysis

Shared code base for Omniroute experiment data preprocessing and analysis.

Environment Setup

Use within a conda environment omniroute_analysis that you create using:

conda env create -f omniroute_analysis_env.yml

Depending on your terminal run:

conda init powershell

Close and re-open your current shell

Run the following to activate the environment:

conda activate omniroute_analysis_env

Create a .env file in the repo root with the following variables:

TRODES_DIR=
NC4_DATA_DIR=

For example (using double backslashes on Windows paths):

TRODES_DIR=C:\\Users\\lester\\MeDocuments\\Research\\MadhavLab\\Projects\\SpikeGadgets\\Trodes_2-3-4_Windows64
NC4_DATA_DIR=C:\\Users\\lester\\UBC\\Madhav, Manu - lesterkaur2024gate\\analysis\\gate_ephys_test\\data
PYTHONPATH=.

SpikeInterface Setup

Install spikeinterface and related tools using pip:

pip install spikeinterface[full] python-dotenv

Trodes Setup

Download and install the Trodes software suite from the SpikeGadgets website: https://www.spikegadgets.com/trodes

TO DO

• Update .yml to remove unused
• Update .yml to include SpikeInterface

Interpreter Setup (VS Code)

To run scripts with the correct environment:

1. Open the Command Palette (Ctrl+Shift+P)
2. Type Python: Select Interpreter
3. Choose: omniroute_analysis_env (should show path ending in ...\\envs\\omniroute_analysis_env\\python.exe)

Running Preprocessing Scripts

To ensure that all modules (e.g., utils/, pipeline/) are correctly importable, run scripts using Python’s -m module flag from the project root. For example:

python -m experiment.example_experiment.scripts.export_csc_to_matlab

This guarantees that the root folder is treated as the top-level package, avoiding import errors.

Avoid running scripts directly with python path/to/script.py, as this can break relative imports due to how Python sets the module search path.