Metadata-Version: 2.1
Name: napari-aicsimageio
Version: 0.4.0
Summary: AICSImageIO for napari. Multiple file format reading directly into napari using pure Python.
Home-page: https://github.com/AllenCellModeling/napari-aicsimageio
Author: Jackson Maxfield Brown
Author-email: jmaxfieldbrown@gmail.com
License: BSD-3-Clause
Project-URL: Source Code, https://github.com/AllenCellModeling/napari-aicsimageio
Project-URL: Bug Tracker, https://github.com/AllenCellModeling/napari-aicsimageio/issues
Project-URL: Documentation, https://github.com/AllenCellModeling/napari-aicsimageio#README.md
Project-URL: User Support, https://github.com/AllenCellModeling/napari-aicsimageio/issues
Keywords: napari,aicsimageio,TIFF,CZI,LIF,imageio,image reading,metadata
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Framework :: napari
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: setup
Provides-Extra: test
Provides-Extra: dev
License-File: LICENSE

# napari-aicsimageio

[![Build Status](https://github.com/AllenCellModeling/napari-aicsimageio/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/napari-aicsimageio/actions)
[![Code Coverage](https://codecov.io/gh/AllenCellModeling/napari-aicsimageio/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/napari-aicsimageio)

AICSImageIO bindings for napari

---

## Features

-   Supports reading metadata and imaging data for:
    -   `CZI`
    -   `OME-TIFF`
    -   `TIFF`
    -   Any formats supported by [aicsimageio](https://github.com/AllenCellModeling/aicsimageio)
    -   Any additional format supported by [imageio](https://github.com/imageio/imageio)

## Installation

**Stable Release:** `pip install napari-aicsimageio`<br>
**Development Head:** `pip install git+https://github.com/AllenCellModeling/napari-aicsimageio.git`

### Plugin Variants

![screenshot of plugin sorter showing that napari-aicsimageio-in-memory should be placed above napari-aicsimageio-out-of-memory](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/plugin-sorter.png)

There are two variants of this plugin that are added during installation:

-   `aicsimageio-in-memory`, which reads an image fully into memory
-   `aicsimageio-out-of-memory`, which delays reading ZYX chunks until required.
    This allows for incredible large files to be read and displayed.

## Examples of Features

#### General Image Reading

All image file formats supported by
[aicsimageio](https://github.com/AllenCellModeling/aicsimageio) will be read and all
raw data will be available in the napari viewer.

In addition, when reading an OME-TIFF, you can view all OME metadata directly in the
napari viewer thanks to `ome-types`.

![screenshot of an OME-TIFF image view, multi-channel, z-stack, with metadata viewer](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/ome-tiff-with-metadata-viewer.png)

#### Mosaic Reading

When reading CZI or LIF images, if the image is a mosaic tiled image, `napari-aicsimageio`
will return the reconstructed image:

![screenshot of a reconstructed / restitched mosaic tile LIF](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/tiled-lif.png)

#### Multi-Scene Selection

**Experimental**

When reading a multi-scene file, a widget will be added to the napari viewer to manage
scene selection (clearing the viewer each time you change scene or adding the
scene content to the viewer) and a list of all scenes in the file.

![gif of drag and drop file to scene selection and management](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/scene-selection.gif)

## Development

See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.

For additional file format support, contributed directly to
[AICSImageIO](https://github.com/AllenCellModeling/aicsimageio).
New file format support will become directly available in this
plugin on new `aicsimageio` releases.

## Citation

If you find `aicsimageio` _(or `napari-aicsimageio`)_ useful, please cite as:

> AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio

_Free software: BSD-3-Clause_


