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docs(tutorial): restore the napari screenshot cells and result images #53

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45 changes: 40 additions & 5 deletions docs/site/tutorial.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
);
```

<center>
<img src="../_static/_generated/napari_img_and_segmentation.png"
alt="Napari window of multiplexed image and computed segmentation mask"
width=100%
/>
</center>


### Cell-type inference with `deepcell-types`
Expand Down Expand Up @@ -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,
);
```

<center>
<img src="../_static/_generated/napari_celltype_layers.png"
alt="Napari window of multiplexed image with celltype predictions"
width=100%
/>
</center>

[hubmap-data-portal]: https://portal.hubmapconsortium.org/search/datasets
[zarr]: https://zarr.readthedocs.io/en/stable/
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