parallax-app 1.16.1

GUI software for photogrammetry-assisted probe targeting in electrophysiology

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==3.10 (Recommended to install via Anaconda or Miniconda)
  • Python 3.10 is required for the Spinnaker library.
• Spinnaker SDK 4.2

Installation

1. Create a virtual environment with Python 3.10 and activate it:
2. Install Parallax:

pip install parallax-app

To upgrade to the latest version, run:

pip install parallax-app --upgrade

3. Install the camera interface Spinnaker SDK 4.2

# Install from the **wheel file** that comes with the Spinnaker SDK ver.4.2.
# Replace **<WHEEL_PATH>** with the *full path* to your `.whl`:
pip install "<WHEEL_PATH>"

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

1. Clone the repository if it hasn't been done already.

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

2. 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

3. Verify your folder structure looks like this:

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

For developers:

1. Clone the repository:

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

2. Install the package along with dev dependencies:

pip install -e .[dev]

Documentation

1. To install the dependencies:

pip install -e .[docs]

2. 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.