semvec/pypi-packages huggingface dataset:
nviz 0.0.5
A tool for creating and visualizing n-dimensional microscopy images.
Requires Python: >=3.11

# nViz

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![Coverage Status](https://raw.githubusercontent.com/WayScience/nViz/main/docs/src/_static/coverage-badge.svg)
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This project focuses on ingesting a set of [TIFF](https://en.wikipedia.org/wiki/TIFF) images as [OME-Zarr](https://pmc.ncbi.nlm.nih.gov/articles/PMC9980008/) or [OME-TIFF](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47).
Each input image set[<sup>1</sup>](#image_set_ref) are organized by channel and z-slices which form four dimensional (4D) microscopy data.
These 4D microscopy data contain information for biological objects (such as organoids).

We read the output with [Napari](https://napari.org/dev/index.html), which provides a way to analyze and understand the 3D image data.

> <a name="image_set_ref">1.</a> __Image set__ is loosely defined and changes depending on the context of the data.
> Here it represents a set of images in multiple dimensions that contain information regarding the same sample.
> Each image in an imageset is paired data and must be related as such.

## Installation

Install nViz from [PyPI](https://pypi.org/project/nViz/) or from source:

```shell
# install from pypi
pip install nviz

# install directly from source
pip install git+https://github.com/WayScience/nViz.git
```

### Installation notes for Linux

`nViz` leverages Napari to help render visuals.
Napari leverages [PyQT](https://riverbankcomputing.com/software/pyqt/intro) to help build graphical components.
PyQT has specific requirements based on the operating system which sometimes can cause errors within Napari, and as a result, also `nViz`.

Below are some steps to try if you find that `nViz` visualizations through Napari are resulting in QT-related errors.

- Attempt to install `python3-pyqt5` through your system package manager (e.g. `apt install python3-pyqt5`).
- When using `nViz` within GitHub Actions Linux environments, consider using [pyvista/setup-headless-display-action](https://github.com/pyvista/setup-headless-display-action) with `qt: true` in order to run without general exceptions.

## Contributing, Development, and Testing

Please see our [contributing](https://WayScience.github.io/coSMicQC/main/contributing) documentation for more details on contributions, development, and testing.