diff --git a/docs/site/tutorial.md b/docs/site/tutorial.md index dfa7a19..ef0a516 100644 --- a/docs/site/tutorial.md +++ b/docs/site/tutorial.md @@ -247,8 +247,26 @@ mask_lyr = nim.add_labels(mask, name="CellSAM segmentation") mask_lyr.contour = 3 # Relatively thick borders for static viz ``` -The image and segmentation layers appear directly in the interactive Napari -viewer. Static documentation builds do not execute or embed GUI screenshots. +```{code-cell} ipython3 +:tags: [hide-cell] + +# For static rendering - can safely be ignored if running notebook interactively +from pathlib import Path + +screenshot_path = Path("../_static/_generated") +screenshot_path.mkdir(parents=True, exist_ok=True) +nim.screenshot( + path=screenshot_path / "napari_img_and_segmentation.png", + canvas_only=False, +); +``` + +
+ Napari window of multiplexed image and computed segmentation mask +
### Cell-type inference with `deepcell-types` @@ -401,9 +419,26 @@ for k, l in labels_by_celltype.items(): ) ``` -When running interactively, the new label layers appear directly in the Napari -viewer and can be toggled independently. Static documentation builds do not -execute or embed GUI screenshots. +```{code-cell} ipython3 +:tags: [hide-cell] + +# For static rendering - can safely be ignored if running notebook interactively +from pathlib import Path + +screenshot_path = Path("../_static/_generated") +screenshot_path.mkdir(parents=True, exist_ok=True) +nim.screenshot( + path=screenshot_path / "napari_celltype_layers.png", + canvas_only=False, +); +``` + +
+ Napari window of multiplexed image with celltype predictions +
[hubmap-data-portal]: https://portal.hubmapconsortium.org/search/datasets [zarr]: https://zarr.readthedocs.io/en/stable/