pyphenix 0.3.3

A data loader and widget to visualize high-dimensional data collected on the Opera Phenix

pyphenix

A data loader and widget to visualize high-dimensional data collected on the Opera Phenix

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This napari plugin was generated with copier using the napari-plugin-template (None).

Installation

Using napari's graphical plugin manager

Users can entirely avoid using a command prompt by using the package manager built in to the bundled napari app.

Follow the installation instructions to download and install the correct version of the bundled napari app for your operating systems (MacOS, Windows, or Linux).

Then following the instructions for installing plugins, search for PyPhenix in the Plugin Manager search bar and click "Install".

Using Python package installer (pip)

Reader only (no GUI, no napari required)

If you only need the OperaPhenixReader — for example on a server or in a headless analysis pipeline — install the base package:

pip install pyphenix

This installs only numpy and Pillow. napari, Qt, and pandas are not required and will not be installed.

from pyphenix import OperaPhenixReader

reader = OperaPhenixReader("/path/to/experiment")
data, metadata = reader.read_data(row="D", column=4)

Full GUI install (napari widget)

To use the interactive napari widget, install with the napari extra:

pip install "pyphenix[napari]"

This additionally installs napari, qtpy, and pandas.

from pyphenix import launch_viewer

viewer, widget = launch_viewer("/path/to/experiment")

Alternatively, if napari is already installed in your environment, the base install is sufficient — pyphenix will detect napari at import time and make the widget available automatically:

pip install pyphenix

Latest development version

pip install git+https://github.com/ferrinm/pyphenix.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the GNU GPL v3.0 license, "pyphenix" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.