parallax-app

Parallax

Parallax is a graphical user interface designed to streamline the process of setting up and performing acute in vivo electrophysiology experiments.

Documentation: parallax.readthedocs.io.

Prerequisites

• Python==3.8 (Recommended to install via Anaconda or Miniconda)
  • Python 3.8 is required for the Spinnaker library.
• PySpin (for Linux or Mac OS users)
• Spinnaker SDK

Installation

• Create a virtual environment with Python 3.8 and activate it:

• On Windows:

conda create -n parallax python=3.8
conda activate parallax

• To install Parallax into a fresh environment, run:

pip install parallax-app

To upgrade to the latest version, run:

pip install parallax-app --upgrade

• To install the camera interface:

pip install parallax-app[camera]

Additional Setup for Linux and macOS

• Download the Spinnaker SDK package for your system here
• Follow the installation instructions in the README
• Install the Python bindings found alongside the SDK package

Running Parallax

python -m parallax

Optional: Enable SuperPoint + SuperGlue Reticle Detection

Parallax supports reticle detection using SuperPoint + LightGlue. To enable reticle detection using SuperPoint + SuperGlue, you must manually download 'SuperGluePretrainedNetwork' pretrained models.

The SuperGluePretrainedNetwork is not included in this repository and is distributed under its own licensing terms. Please review their license before use.

Manual Setup Instructions Clone the repository into the external/ folder in your Parallax project root:

pip install git+https://github.com/AllenNeuralDynamics/sfm.git@main
git clone https://github.com/magicleap/SuperGluePretrainedNetwork.git external/SuperGluePretrainedNetwork

Verify your folder structure looks like this:

parallax/
├── external/
│   └── SuperGluePretrainedNetwork/
│       └── models/
│           ├── superpoint.py
│           └── weights/
│               ├── superpoint_v1.pth
│               └── superglue_indoor.pth

For developers:

• Clone the repository:

git clone https://github.com/AllenNeuralDynamics/parallax.git

• Install the package along with dev dependencies:

pip install -e .[dev]

Documentation

• To install the dependencies:

pip install -e .[docs]

• Then to create the documentation html files, run:

sphinx-build -b html docs/ docs/_build

Support and Contribution

If you encounter any problems or would like to contribute to the project, please submit an Issue on GitHub.

License

Parallax is licensed under the MIT License. For more details, see the LICENSE file.