Metadata-Version: 2.4
Name: napari-stitcher
Version: 0.1.2
Summary: Stitch napari image layers in 2-3D+t
Author: Marvin Albert
Author-email: marvin.albert@gmail.com
License: BSD-3-Clause
Project-URL: Bug Tracker, https://github.com/multiview-stitcher/napari-stitcher/issues
Project-URL: Documentation, https://multiview-stitcher.github.io/napari-stitcher/
Project-URL: Source Code, https://github.com/multiview-stitcher/napari-stitcher
Project-URL: User Support, https://github.com/multiview-stitcher/napari-stitcher/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: dask
Requires-Dist: magicgui
Requires-Dist: multiscale_spatial_image
Requires-Dist: multiview-stitcher>=0.1.24
Requires-Dist: napari
Requires-Dist: numpy>=1.18
Requires-Dist: qtpy
Requires-Dist: spatial_image
Requires-Dist: tifffile>=2022.7.28
Requires-Dist: tqdm
Requires-Dist: xarray
Provides-Extra: testing-no-gui
Requires-Dist: tox; extra == "testing-no-gui"
Requires-Dist: multiview-stitcher[czi]>=0.1.24; extra == "testing-no-gui"
Requires-Dist: pytest; extra == "testing-no-gui"
Requires-Dist: pytest-cov; extra == "testing-no-gui"
Requires-Dist: pytest-qt; extra == "testing-no-gui"
Provides-Extra: testing
Requires-Dist: tox; extra == "testing"
Requires-Dist: multiview-stitcher[czi]>=0.1.24; extra == "testing"
Requires-Dist: pytest; extra == "testing"
Requires-Dist: pytest-cov; extra == "testing"
Requires-Dist: pytest-qt; extra == "testing"
Requires-Dist: napari; extra == "testing"
Requires-Dist: pyqt5; extra == "testing"
Dynamic: license-file

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# napari-stitcher

A napari plugin for stitching large multi-positioning datasets in 2/3D+t using [`multiview-stitcher`](https://github.com/multiview-stitcher/multiview-stitcher).

![](docs/images/napari-stitcher-loaded-mosaic-annotated.png)
<small>Image data by Arthur Michaut @ Jérôme Gros Lab @ Institut Pasteur.</small>

#### Quick guide:

1. Directly stitch napari layers: Use napari to load, visualize and [preposition](prearrangement.md) the tiles to be stitched.
2. When working with multi-channel data, stick to the following [naming convention](naming_convention.md): `{tile} :: {channel}`.
3. Load either all or just a subset of the layers into the plugin.
4. Choose registration options: registration channel, binning and more.
5. Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).
6. The registration result is shown in the viewer and the fused channels are added as new layers.

## Demo

https://github.com/user-attachments/assets/8773e49f-af18-4ff3-ab2f-2a5f1b1cadf2

<small>This demo uses the awesome [`napari-threedee`](https://github.com/napari-threedee/napari-threedee) for prepositioning the tiles. Image data: [BigStitcher](https://imagej.net/plugins/bigstitcher/).</small>

## Documentation

Head over to the [user guide](https://multiview-stitcher.github.io/napari-stitcher/main/) for more details.

## Installation

You can install `napari-stitcher` via `pip`:

```bash
pip install napari-stitcher
```

For more installation options, see the [installation docs](https://multiview-stitcher.github.io/napari-stitcher/main/installation/).

## Contributing

Contributions are very welcome. Tests can be run with `tox`.

## License

Distributed under the terms of the [BSD-3] license, "napari-stitcher" is free and open source software

## Issues

If you encounter any problems, please [file an issue](https://github.com/multiview-stitcher/napari-stitcher/issues) along with a detailed description.
