diff --git a/README.md b/README.md index 8ec10d4..1fe316f 100644 --- a/README.md +++ b/README.md @@ -9,24 +9,57 @@ A plugin to read whole-slide images within [napari]. --- -## Installation +## Installation via pip You can install `napari-wsi` via [pip]: ```bash -pip install napari-wsi[all] +pip install "napari-wsi[all]>=1.0" ``` This automatically installs all optional backends, as a shortcut for: ```bash -pip install napari-wsi[openslide,rasterio,wsidicom] +pip install "napari-wsi[openslide,rasterio,wsidicom]>=1.0" ``` In addition, to be able to read images using the `openslide` backend, it is required to install the OpenSlide library itself, for example by installing the [openslide-bin] python package (also via [pip]). +## Installation via conda + +To set up a new [conda] environment for `napari-wsi` that also includes all +optional dependencies, create a new file named `napari-wsi.yml` with the +following content: + +```yaml +name: napari-wsi +channels: + - conda-forge +dependencies: + - python=3.11 + - napari-wsi=1.* + # napari + - napari + - pyqt + # openslide backend + - openslide>=4.0 + - openslide-python>=1.4 + # rasterio backend + - rasterio>=1.4 + - pip: + # wsidicom backend + - wsidicom>=0.22 + - numpy<=2.1 # for numba +``` + +Then create this environment by running: + +```bash +conda env create -f napari-wsi.yml +``` + # Description This [napari] plugin provides a widget for reading various whole-slide image @@ -62,6 +95,7 @@ viewer = Viewer() viewer.open("CMU-1.svs", plugin="napari-wsi") ``` +[conda]: https://conda-forge.org/ [napari]: https://github.com/napari/napari [openslide]: https://github.com/openslide/openslide-python [openslide-bin]: https://pypi.org/project/openslide-bin/