From 34abf61cd7112a8043238c839f746c7a73ea26f1 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 30 Jul 2024 17:08:50 +0100 Subject: [PATCH] Update references to plugin names (#228) --- docs/source/tutorials/cellfinder-detection.md | 6 +++--- docs/source/tutorials/cellfinder-retraining.md | 6 +++--- docs/source/tutorials/tutorial-whole-brain-registration.md | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/source/tutorials/cellfinder-detection.md b/docs/source/tutorials/cellfinder-detection.md index abc181b2..eac85e79 100644 --- a/docs/source/tutorials/cellfinder-detection.md +++ b/docs/source/tutorials/cellfinder-detection.md @@ -16,7 +16,7 @@ You will need `napari` installed on your computer - please follow ::: 1. Open `napari`. -2. Install `cellfinder` by selecting `Plugins > Install/Uninstall plugins` and searching for `cellfinder-napari` in the searchbox. If it is not installed yet, click on the `Install` button. +2. Install `cellfinder` by selecting `Plugins > Install/Uninstall plugins` and searching for `cellfinder` in the searchbox. If it is not installed yet, click on the `Install` button. :::{caution} This may take a while due to the various dependencies being installed. @@ -24,12 +24,12 @@ This may take a while due to the various dependencies being installed. On Silicon Macs you may have to run `conda install hdf5` on the command line (in your conda environment) first for the installation to be successful. ::: -3. Open the cell detection widget by selecting `Plugins > cellfinder-napari > Cell detection` in the napari menu bar near the top left of the window. +3. Open the cell detection widget by selecting `Plugins > cellfinder > Cell detection` in the napari menu bar near the top left of the window. ![cellfinder detection widget](./images/cellfinder-napari/cellfinder-napari-detection.png) **The cell detection widget appears on the right-hand side of the window.** -4. Load some sample data `File > Open sample > Sample data (cellfinder-napari)`. This will open a small two-channel 3D image. +4. Load some sample data `File > Open sample > Sample data (cellfinder)`. This will open a small two-channel 3D image. 5. Set the `signal image` to `Signal` 6. Set the `background image` to `Background` 7. Ensure that `Voxel size (z)` is set to `5.00`, `Voxel size (y)` is set to `2.00`, and `Voxel size (x)` is set to `2.00`. diff --git a/docs/source/tutorials/cellfinder-retraining.md b/docs/source/tutorials/cellfinder-retraining.md index 06ec473f..f74203b2 100644 --- a/docs/source/tutorials/cellfinder-retraining.md +++ b/docs/source/tutorials/cellfinder-retraining.md @@ -18,8 +18,8 @@ You will need `napari` installed on your computer - please follow ::: 1. Open `napari`. -2. Open the curation widget by selecting `Plugins > cellfinder-napari > Curation` in the napari menu bar near the top left of the window. -3. Load some sample data `File > Open sample > Sample data (cellfinder-napari)`. This will open the same small two-channel 3D image from the detection tutorial. +2. Open the curation widget by selecting `Plugins > cellfinder > Curation` in the napari menu bar near the top left of the window. +3. Load some sample data `File > Open sample > Sample data (cellfinder)`. This will open the same small two-channel 3D image from the detection tutorial. 4. Click `Files > Open File(s)` and select the `cells.xml` from the detection tutorial. If napari prompts you to choose a plugin, choose `brainglobe-napari-io`. 5. Set the `signal image` to `Signal` 6. Set the `background image` to `Background` @@ -35,7 +35,7 @@ widget, or pressing the `3` key on your keyboard. 11. Click `Save training data` 12. Create and then select a new directory on your computer (e.g. `cellfinder-retraining`) and click `Choose`. 13. Close the curation widget by clicking the `x` at the top left of the widget. -14. Open the retraining widget by selecting `Plugins > cellfinder-napari > Train network` in the napari menu bar near the top left of the window. +14. Open the retraining widget by selecting `Plugins > cellfinder > Train network` in the napari menu bar near the top left of the window. 15. Select the data for retraining by clicking `Select files` next to `YAML files` and choose the `training.yml` file is inside the `cellfinder-retraining` directory created earlier 16. Choose a directory to save the training output, e.g., create a `trained_network` directory diff --git a/docs/source/tutorials/tutorial-whole-brain-registration.md b/docs/source/tutorials/tutorial-whole-brain-registration.md index 180d3a29..b96e1e24 100644 --- a/docs/source/tutorials/tutorial-whole-brain-registration.md +++ b/docs/source/tutorials/tutorial-whole-brain-registration.md @@ -11,8 +11,8 @@ You will need `napari` installed on your computer - please follow [`napari`'s in ::: 1. Open `napari`. -2. Install `brainreg-napari` by selecting `Plugins > Install/Uninstall plugins` and searching for `brainreg-napari` in the searchbox. Then click on the `Install` button. -3. Open the `brainreg` widget by selecting `Plugins > Atlas registration (brainreg-napari)` in the napari menu bar near the top left of the window. +2. Install `brainreg` by selecting `Plugins > Install/Uninstall plugins` and searching for `brainreg` in the searchbox. Then click on the `Install` button. +3. Open the `brainreg` widget by selecting `Plugins > Atlas registration (brainreg)` in the napari menu bar near the top left of the window. ![brainreg widget](./images/brainreg-napari/plugin-menu-brainreg-napari.png) **The brainreg widget appears on the right-hand side of the window.**