From e0ce825ca19ddc6ba41396309ed40ab9ddf44087 Mon Sep 17 00:00:00 2001 From: Alessandro Felder Date: Tue, 30 Jul 2024 13:35:33 +0100 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Adam Tyson --- .../brainglobe-atlasapi/usage/command-line-interface.md | 2 ++ docs/source/tutorials/index.md | 2 +- docs/source/tutorials/visualise-atlas-napari.md | 3 ++- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/source/documentation/brainglobe-atlasapi/usage/command-line-interface.md b/docs/source/documentation/brainglobe-atlasapi/usage/command-line-interface.md index 81b5d0f5..e25fe2c7 100644 --- a/docs/source/documentation/brainglobe-atlasapi/usage/command-line-interface.md +++ b/docs/source/documentation/brainglobe-atlasapi/usage/command-line-interface.md @@ -18,5 +18,7 @@ brainglobe update -a allen_mouse_25um Further instructions can be found by running `brainglobe --help`. +:::{hint} We also provide a [graphical user interface](/tutorials/manage-atlases-in-GUI) to download and update atlases, as part of the `brainrender-napari` package. +::: diff --git a/docs/source/tutorials/index.md b/docs/source/tutorials/index.md index 19a665aa..0be8a87d 100644 --- a/docs/source/tutorials/index.md +++ b/docs/source/tutorials/index.md @@ -9,7 +9,7 @@ :img-bottom: images/atlas-versions.png :link: manage-atlases-in-GUI :link-type: doc -Download an atlas through napari +Download an atlas with napari ::: :::{grid-item-card} {fas}`brain;sd-text-primary` Atlas visualisation diff --git a/docs/source/tutorials/visualise-atlas-napari.md b/docs/source/tutorials/visualise-atlas-napari.md index f6ea18c6..e13ff341 100644 --- a/docs/source/tutorials/visualise-atlas-napari.md +++ b/docs/source/tutorials/visualise-atlas-napari.md @@ -36,13 +36,14 @@ If you've not used BrainGlobe atlases before, you will need to download those yo ![brainrender widget with region mesh](./images/brainrender-napari/add-region-brainrender-napari.png) **You have now added a 3D atlas region mesh layer, which appears as a mesh in the viewer and as a new layer in the layers list.** + 7. Back in the "Atlas Viewer" section, right-click on the `mpin_zfish_1um` row. In the menu that appears, select `GAD1b`. ![brainrender widget with additional reference](./images/brainrender-napari/additional-reference-brainrender-napari.png) **You have now added an additional reference image, which appears as a grey scale image in the viewer and as a new layer in the layers list.** -You have now added all possible kinds of BrainGlobe atlas components (annotations image, reference image, 3D atlas region mesh, additional reference) to napari - well done! You can now add any of the other atlases listed in the `Atlas Viewer` section if you like (note that not all atlases have additional references!). +You have now added all possible kinds of BrainGlobe atlas components (annotations image, reference image, 3D atlas region mesh, additional reference) to napari! You can now add any of the other atlases listed in the `Atlas Viewer` section if you like (note that not all atlases have additional references!). :::{note} Hover over any of the elements in the `brainrender` widget to get additional hints about how to use them!