final link-fixing/rename to brainglobe-segmentation

docs/source/documentation/brainreg-segment/index.md → docs/source/documentation/brainglobe-segmentation/index.md

@@ -1,25 +1,25 @@
-# brainreg-segment
+# brainglobe-segmentation
 
 
-brainreg-segment is a companion to [brainreg](../brainreg/index) allowing manual segmentation of regions/objects 
+brainglobe-segmentation is a companion to [brainreg](../brainreg/index) allowing manual segmentation of regions/objects 
 within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, 
 and visualisation (e.g. in [brainrender](../brainrender/index)).
 
 ## Installation
 
-brainreg-segment comes bundled with brainreg, so see the [brainreg installation instructions](../brainreg/installation). 
-brainreg-segment can be installed on its own (see below), but you will need to register your data with brainreg first.
+brainglobe-segmentation comes bundled with brainreg's optional `napari` dependency, so see the [brainreg installation instructions](../brainreg/installation). 
+brainglobe-segmentation can be installed on its own (see below), but you will need to register your data with brainreg first.
 
 ### Standalone installation
 
-If you don't want to install brainreg, brainreg-segment can be installed on its own. brainreg-segment is 
+If you don't want to install brainreg, brainglobe-segmentation can be installed on its own. brainglobe-segmentation is 
 distributed as a plugin for [napari](https://napari.org/), so first follow the 
-[napari installation instructions](https://napari.org/). You can then install `brainreg-segment` from the 
+[napari installation instructions](https://napari.org/). You can then install `brainglobe-segmentation` from the 
 napari plugin menu.
 
 ![Installing from the napari plugin menu](images/install_plugin.png)
 
-Alternatively, the plugin can be installed into a Python environment with `pip install brainreg-segment`.
+Alternatively, the plugin can be installed into a Python environment with `pip install brainglobe-segmentation`.
 
 
 ## User guide
@@ -34,7 +34,7 @@ user-guide/analysing-external-segmentation
 
 ## Citation
 
-If you find brainreg-segment useful and use it in your research, please let us know and also cite the paper:
+If you find brainglobe-segmentation (formerly brainreg-segment) useful and use it in your research, please let us know and also cite the paper:
 
 > Tyson, A. L., Vélez-Fort, M.,  Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T.,  Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)
 

docs/source/documentation/brainreg-segment/user-guide/analysing-external-segmentation.md → docs/source/documentation/brainglobe-segmentation/user-guide/analysing-external-segmentation.md

@@ -8,14 +8,14 @@ Plugins exist to segment
  many features common to biomedical images, and their results can be incorporated with BrainGlobe to analyse 
 the distribution of features of interest within the context of an anatomical atlas. 
 
-To be compatible with `brainreg-segment`, the third-party napari plugin must be able to take a 3D image layer as 
+To be compatible with `brainglobe-segmentation`, the third-party napari plugin must be able to take a 3D image layer as 
 input and return one of:
 - A 3D labels layer with either a 2 or 3D region labeled (e.g., segmenting bulk axonal projections)
 - A 3D points layer with a series of points corresponding to a trajectory through 3D space
 
 :::{hint}
-It is possible to segment structures outside the `brainreg-segment` plugin and import them in later (e.g., by 
-saving to a `.tiff` and reloading). However, it is simpler to load the data using `brainreg-segment` and then segment 
+It is possible to segment structures outside the `brainglobe-segmentation` plugin and import them in later (e.g., by 
+saving to a `.tiff` and reloading). However, it is simpler to load the data using `brainglobe-segmentation` and then segment 
 it using a third-party plugin. This ensures that the coordinate spaces you are using are consistent. 
 :::
 
@@ -25,7 +25,7 @@ it using a third-party plugin. This ensures that the coordinate spaces you are u
 - Open napari
 - Install the napari plugin you require to segment your data. To find out which plugins are available, see the 
 [napari hub](https://www.napari-hub.org/).
-- [Load your data using the `brainreg-segment` plugin](/documentation/brainreg-segment/user-guide/index)
+- [Load your data using the `brainglobe-segmentation` plugin](/documentation/brainglobe-segmentation/user-guide/index)
 - Use the plugin to segment your feature of interest. Ensure it returns a 3D labels or points layer.
 
 :::{hint}
@@ -48,8 +48,8 @@ At this point you could load a layer segmented previously and saved to disk
 ![Highlighting a specific layer](../images/layerlist.png)
 
 - Click either the `Add track from selected layer` or `Add region from selected layer` button as applicable. This will
-add the region/points from the layer to the `brainreg-segment` analysis list (in the same way as if it had been 
-analysed manually within `brainreg-segment`).
+add the region/points from the layer to the `brainglobe-segmentation` analysis list (in the same way as if it had been 
+analysed manually within `brainglobe-segmentation`).
 - Follow the instructions for either:
   - [1D track analysis](segmenting-1d-tracks)
   - [2/3D region analysis](segmenting-3d-structures)

docs/source/documentation/brainreg-segment/user-guide/index.md → docs/source/documentation/brainglobe-segmentation/user-guide/index.md

@@ -9,11 +9,11 @@ downsampled (e.g., using the `--downsample` flag in brainreg).
 # Usage
 
 To load the software, firstly open napari (typically by typing `napari` into your command window). You can then 
-load `brainreg-segment` by navigating to `Plugins` -> `Add Dock Widget` and selecting `brainreg-segment`.
+load `brainglobe-segmentation` by navigating to `Plugins` -> `Add Dock Widget` and selecting `brainglobe-segmentation`.
 
 The plugin will then open, with some options for loading data:
 
-![brainreg interface](../images/brainreg-segment.webp)
+![brainreg interface](../images/brainglobe-segmentation.webp)
 
 ## **To load your data**
 

docs/source/documentation/brainreg/installation.md

@@ -16,11 +16,11 @@ Whichever interface you use, the results will be identical.
 :::{admonition} Installing the napari plugin
 :class: dropdown
 * [Make sure you have napari installed](https://napari.org/stable/tutorials/fundamentals/installation.html)
-* Install the brainreg-napari plugin from within napari (`Plugins` -> `Install/Uninstall Package(s)`, choosing `brainreg-napari`).)
+* Install the brainreg napari plugin from within napari (`Plugins` -> `Install/Uninstall Package(s)`, choosing `brainreg`).)
 
 :::{note}
 If you are using macOS, you will need to install the plugin using the
-command line (`conda install -c conda-forge brainreg-napari`)
+command line (`conda install -c conda-forge brainreg`)
 :::
 
 :::{admonition} Installing the command line tool
@@ -49,6 +49,7 @@ Remember to activate your conda environment before doing anything
 ```
 
 ### Using conda (recommended)
+This includes the napari plugin.
 
 ```bash
 conda install -c conda-forge brainreg

docs/source/documentation/brainreg/user-guide/output-files.md

@@ -1,6 +1,6 @@
 # Output files
 
-brainreg will create a number of output files. Many of these are for use with other software (e.g., brainreg-segment 
+brainreg will create a number of output files. Many of these are for use with other software (e.g., brainglobe-segmentation 
 and cellfinder), but they may be useful for your own software.
 
 :::{note}
@@ -9,7 +9,7 @@ N.B. This is not an exhaustive list, as brainreg has many options which may crea
 
 * `boundaries.tiff` - A 3D tiff image of the atlas boundaries, transformed to the space of the raw data.
 * `brainreg_DATE_TIME.log` - A log file detailing the registration process. Useful for debugging and raising issues.
-* `brainreg.json` - A record of all the input parameters, used by other software, e.g. brainreg-segment.
+* `brainreg.json` - A record of all the input parameters, used by other software, e.g. brainglobe-segmentation.
 * `deformation_field_0.tiff` - A 3D tiff describing the deformation from raw data space to atlas space, in the first 
 dimension (based on the supplied orientation and voxel sizes).
 * `deformation_field_1.tiff` - Deformation in the second dimension.

docs/source/documentation/index.md

@@ -6,7 +6,7 @@ setting-up/index
 bg-atlasapi/index
 bg-space/index
 brainreg/index
-brainreg-segment/index
+brainglobe-segmentation/index
 brainrender/index
 cellfinder/index
 morphapi/index

docs/source/publications.md

@@ -1,6 +1,6 @@
 # Publications
 
-Brainreg & brainreg-segment:
+Brainreg & brainglobe-segmentation (formerly brainreg-segment):
 > Tyson, A. L., Vélez-Fort, M.,  Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022) “Accurate determination of marker location within whole-brain microscopy images" Scientific Reports, [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)
 
 3D cell detection:

docs/source/tutorials/silicon-probe-tracking.md

@@ -20,7 +20,7 @@ micromanipulator, and the probe tip lowered to touch the surface of the brain (e
 This position is recorded as position “zero”. The probe is then introduced in the brain at a speed of \~10μm 
 per second to the desired penetration depth (in our case 1750μm; **Fig. 1**, centre).
 
-![Figure 1.](./images/brainreg-segment-fig1.webp)
+![Figure 1.](./images/brainglobe-segmentation-fig1.webp)
 **Figure 1.**
 
 :::{note}
@@ -80,11 +80,11 @@ trace the probe track.
 Make sure your conda environment is still activated!
 :::
 
-To open the graphical user interface, open napari and then load the `brainreg-segment` plugin (see 
-[User guide](/documentation/brainreg-segment/user-guide/index)).
+To open the graphical user interface, open napari and then load the `brainglobe-segmentation` plugin (see 
+[User guide](/documentation/brainglobe-segmentation/user-guide/index)).
 
-The `brainreg-segment`graphical user interface opens and shows a set of tools.You can then load your brainreg output 
-directory, and follow the main brainreg-segment instructions [here](/documentation/brainreg-segment/user-guide/segmenting-1d-tracks) for 
+The `brainglobe-segmentation`graphical user interface opens and shows a set of tools.You can then load your brainreg output 
+directory, and follow the main brainglobe-segmentation instructions [here](/documentation/brainglobe-segmentation/user-guide/segmenting-1d-tracks) for 
 segmenting a 1D track. Setting `Spline points` will determine how many times along the length of the track that 
 the brain region is sampled at. This can be used to determine the brain region for each recording site on your probe.
 

docs/source/tutorials/tracing-tracking.md

@@ -88,14 +88,14 @@ the Otsu[^1] thresholding method from `napari-simpleitk-image-processing` an exa
 To use Otsu's method from the `napari-simpleitk-image-processing` plugin, follow these steps:
 
 - Open napari
-- [Load your data using the `brainreg-segment` plugin](/documentation/brainreg-segment/user-guide/index)
+- [Load your data using the `brainglobe-segmentation` plugin](/documentation/brainglobe-segmentation/user-guide/index)
 - Choose the Otsu thresholding option from the plugin menu:
 
 <img src="./images/choose-otsu.png"  width="450">
 
 - Select the image layer to be thresholded and click `run`. This will automatically segment your image using Otsu's
 algorithm. This will create a new labels layer. 
-- Follow the instructions for [2/3D region analysis](/documentation/brainreg-segment/user-guide/segmenting-3d-structures) 
+- Follow the instructions for [2/3D region analysis](/documentation/brainglobe-segmentation/user-guide/segmenting-3d-structures) 
 to analyse the distribution of the thresholded voxels.
 
 **Instructions by** [**Sara Mederos**](https://www.sainsburywellcome.org/web/people/sara-mederos).