From 6b6ba0956c939f408f44317da9bfc5a8d6194bd2 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 24 Oct 2023 13:23:05 +0100 Subject: [PATCH] Remove documentation about disabled brainglobe-napari-io functionality --- .../brainreg/user-guide/visualisation.md | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/docs/source/documentation/brainreg/user-guide/visualisation.md b/docs/source/documentation/brainreg/user-guide/visualisation.md index 5af50bb5..c816a75f 100644 --- a/docs/source/documentation/brainreg/user-guide/visualisation.md +++ b/docs/source/documentation/brainreg/user-guide/visualisation.md @@ -3,8 +3,6 @@ If you have used the brainreg command-line interface, or simply want to view res brainreg comes with a plugin for napari to allow you to easily view registration results. ## Usage -Typically, you would view the results in sample space, i.e. with registration results overlaid on your data. - To begin, open napari and drag your brainreg output directory (the one with the log file) onto the napari window. Various images should then open, including: @@ -22,17 +20,3 @@ N.B. If you use a high-resolution atlas (such as `allen_mouse_10um`), then the f ::: ![Visualisation in sample space](/documentation/brainreg/images/sample_space.gif) - -## Atlas space - -`napari-brainreg` also comes with an additional plugin, for visualising your data in atlas space, -i.e., where your data is warped to the atlas coordinate space. - -This is typically only used in other software, but you can enable it yourself: - -* Open napari -* Navigate to `Plugins` -> `Plugin Call Order` -* In the `Plugin Sorter` window, select `napari_get_reader` from the `select hook...` dropdown box -* Drag `brainreg_read_dir_standard_space` (the atlas space viewer plugin) above `brainreg_read_dir` -(the normal plugin) to ensure that the atlas space plugin is used preferentially. -