ideas-toolbox-suite2p

Table of Contents

• Toolbox Description
• Navigating the Project Repository
• Usage Instructions
  • List available commands
  • Build Docker image
  • Clean project
  • Run a specific tool
  • Run jupyterlab inside the docker container
  • Run tests

Toolbox Description

A toolbox for running suite2p-based tools on the IDEAS platform.

This toolbox is designed to run as a Docker image, which can be run on the IDEAS platform. This toolbox consists of the following tools:

• Suite2p end-to-end pipeline: Run the suite2p pipeline to extract calcium traces.
• Binary Conversion: Convert raw 2p input movie(s) into a suite2p binary file.
• Registration: Run suite2p registration on a raw suite2p binary movie.
• ROI Detection: Run suite2p ROI detection on a raw suite2p binary movie.
• ROI Extraction: Extract calcium traces from suite2p binary movie(s).
• ROI Classification: Run suite2p ROI classification on extracted ROIs.
• Spike Deconvolution: Run suite2p spike deconvolution on extracted fluorescence traces.
• Output Conversion: Output suite2p results in specific formats

How to Get Help

• IDEAS documentation contains detailed information on how to use the toolbox within the IDEAS platform, the parameters that can be used, and the expected output.
• If you have found a bug, we reccomend searching the issues page to see if it has already been reported. If not, please open a new issue.
• If you have a feature request, please open a new issue with the label enhancement

Executing the Toolbox

To run the toolbox, you can use the following command:

make run TOOL=<tool_name>

Available tools are:

• suite2p_wrapper__run_suite2p_end_to_end
• suite2p_individual_steps__suite2p_binary_conversion
• suite2p_individual_steps__suite2p_registration
• suite2p_individual_steps__suite2p_roi_detection
• suite2p_individual_steps__suite2p_roi_extraction
• suite2p_individual_steps__suite2p_roi_classification
• suite2p_individual_steps__suite2p_spike_deconvolution
• suite2p_individual_steps__suite2p_output_conversion

The command will excute the tool with inputs specified in the inputs folder. The output will be saved in the outputs folder.

Navigating the Project Repository

├── commands                # Standardized scripts to execute tools on the cloud
├── data                    # Small data files used for testing
├── info                    # Files describing the toolbox & tools for the IDEAS system
├── inputs                  # Predefined test inputs for the command scripts
│── toolbox                 # Contains all code for running and testing the tools
│   ├── tools               # Contains the individual analysis tools
│   ├── utils               # General utilities used by the tools
│   ├── tests               # Unit tests for the individual tools
│── Dockerfile              # Commands to assemble the Docker image
│── Makefile                # To automate and standardize toolbox usage
│── check_tool.sh           # Checks if tool is valid before execution
│── function_caller.py      # Executes tool for IDEAS system
│── pyproject.toml          # Configuration for the python project
│── setup.py                # Specifies dependencies of the python project
│── user_deps.txt           # Specifies user dependencies of the python project
|── LICENSE                 # License file
└── .gitignore              # Tells Git which files & folders to ignore

License

This project is licensed under CC BY-NC 4.0. Note that the software is provided "as is", without warrantee of any kind.

Usage Instructions

List available commands

make help

Build Docker image

make build

Clean project

make clean

Run a specific tool

make run TOOL="tool_name"

Run jupyterlab inside the docker container

make run-jupyter

and navigate to http://localhost:8888 to get a Jupyter environment inside the docker container

Run tests

make test

Test arguments can be specified using TEST_ARGS as shown below. Refer to pytest documentation for supported arguments.

make test TEST_ARGS="-k TestWorkflows"