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Add docs for thick slicing #794
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Uh, it seems that the screenshots generated via code cells are not rendered in the CI's rendered docs. Is that normal? |
It is now! Our CI is now like 3 minutes on here. See napari.org/dev/developers/contributing/documentation/index.html#contributing-to-the-napari-documentation-without-a-local-setup @napari-bot make html |
@psobolewskiPhD make html gave an error https://github.com/napari/docs/actions/runs/16461947669 |
I wonder if it's because you have the command twice? @napari-bot make html |
Looks to be the case. My comment above with text and a single command worked: I can see that with two commands in one comment things get confusing. So let's just not do that 😅 |
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Lastly, `viewer.dims.point` contains the position in world coordinates (i.e., including | ||
scale and translate transformations). | ||
While by default napari will only show data located *exactly* at this position, it is possible to visualize data from a thicker dimensional slice by modifying `viewer.dims.margin_left` and `viewer.dims.margin_right`, or `viewer.dims.thickness` to change both symmetrically (or the corresponding `*_step` properties to work in "slider coordinates"). |
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While by default napari will only show data located *exactly* at this position, it is possible to visualize data from a thicker dimensional slice by modifying `viewer.dims.margin_left` and `viewer.dims.margin_right`, or `viewer.dims.thickness` to change both symmetrically (or the corresponding `*_step` properties to work in "slider coordinates"). | |
By default napari will only show a slice of the data: that which is located *exactly* at this position. However, it is possible to visualize data from a thicker dimensional slice by modifying `viewer.dims.thickness`. This will use each layer's `projection_mode` to visualize the space around `viewer.dims.point`. Alternately, you can set `viewer.dims.margin_left` and `viewer.dims.margin_right` to explicitly set the range of data around `viewer.dims.point` to be projected. Finally, you can use the corresponding `margin_left_step` and `margin_right_step` properties to work in "slider coordinates". |
I found the original very dense and hard to understand. I think this is clearer? But maybe no longer correct 😅
scale and translate transformations). | ||
While by default napari will only show data located *exactly* at this position, it is possible to visualize data from a thicker dimensional slice by modifying `viewer.dims.margin_left` and `viewer.dims.margin_right`, or `viewer.dims.thickness` to change both symmetrically (or the corresponding `*_step` properties to work in "slider coordinates"). | ||
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When margins are non-zero, data is included from before (left) or after (right) the `viewer.dims.point` location, and for each layer it will be projected onto the visible space based on the `projection_mode` of that layer: |
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With my suggestion above, this might be removed.
When margins are non-zero, data is included from before (left) or after (right) the `viewer.dims.point` location, and for each layer it will be projected onto the visible space based on the `projection_mode` of that layer: |
If/once we get the |
References and relevant issues
Description
We finally have decent GUI and programmatic access to thick slicing. This PR adds some info about it in the viewer tutorial.