Improve atlas details within atlas API docs (#249)

.github/workflows/docs_build_and_deploy.yml

@@ -27,7 +27,7 @@ jobs:
     name: Build Sphinx Docs
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/build_sphinx_docs@main
+      - uses: neuroinformatics-unit/actions/build_sphinx_docs@v2
         with:
           check-links: false
 

docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md

@@ -101,6 +101,15 @@ Available versions:
 * `kim_dev_mouse_mri_mtr_10um` - MRI MTR (magnetic transfer ratio) template at 10μm resolution
 * `kim_dev_mouse_mri_t2_10um` - MRI T2 template at 10μm resolution
 
+### [BlueBrain Barrel Cortex Atlas](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00209/121852/Enhancement-of-brain-atlases-with-laminar)
+This atlas from [Bolaños-Puchet et al. (2024)](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00209/121852/Enhancement-of-brain-atlases-with-laminar) 
+is a version of the Allen Adult Mouse Brain Atlas with the addition of annotations of 33 barrels and barrel columns. 
+For more details, please see [the blogpost](/blog/barrel-atlas-added).
+
+Available versions:
+* `allen_mouse_bluebrain_barrels_10um` - 10μm resolution
+* `allen_mouse_bluebrain_barrels_25um` - 25μm resolution
+
 ### [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008)
 This atlas from [Fiederling et al. (2021)](https://doi.org/10.1101/2021.05.06.443008) is a 3D reconstruction of the 
 [Allen Spinal Cord Atlas](https://mousespinal.brain-map.org/).
@@ -119,9 +128,9 @@ Available versions:
 * `osten_mouse_100um` - 100μm resolution
 
 ## Rat
-### [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3)) at 39 micron resolution
+### [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3)
 This atlas is only available at 39μm resolution:
-* `whs_sd_rat_39um` - 39μm resolution
+* `whs_sd_rat_39um`
 
 ## Fish
 ### [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de)
@@ -133,9 +142,22 @@ This atlas is only available at 4μm resolution:
 * `azba_zfish_4um`
 
 ### [Blind Mexican cavefish Brain Atlas](https://elifesciences.org/articles/80777)
+This is a brain atlas of the blind Mexican cavefish (Astyanax mexicanus) from 
+[Kozol et al. (2023)](https://elifesciences.org/articles/80777). For more details please
+see [the blogpost](/blog/cavefish-atlas-added).
+
 This atlas is only available at 2μm resolution:
 * `sju_cavefish_2um`
-
+
+## Amphibian
+### [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3)
+This is a magnetic resonance imaging based atlas of the Axolotl (Ambystoma mexicanum) from 
+[Lazcano et al. (2021)](https://doi.org/10.1038/s41598-021-89357-3). For more details please 
+see [the blogpost](/blog/axolotl-atlas-added).
+
+This atlas is only available at 40μm resolution:
+* `unam_axolotl_40um`
+
 ## Human
 ### [Allen Human Brain Atlas](https://www.brain-map.org)
 This atlas is included mostly for visualisation and comparison to the other atlases. 

docs/source/publications.md

@@ -16,11 +16,9 @@ BrainGlobe Atlas API:
 # Publications citing BrainGlobe
 **This list is automatically generated from Google Scholar**
 
-[//]: # (To generate this, export a list from google scholar as bibtex, then convert to html)
-
-[//]: # ((https://asouqi.github.io/bibtex-converter/) then md (https://codebeautify.org/html-to-markdown&#41). This is a low-tech ))
-
-[//]: # ((way of doing it, but it's much simpler than via the CLIs I found.))
+[//]: # "(To generate this, export a list from google scholar as bibtex, then convert to html)
+((https://asouqi.github.io/bibtex-converter/) then md (https://codebeautify.org/html-to-markdown&#41). This is a low-tech ))
+((way of doing it, but it's much simpler than via the CLIs I found.))"
 
 AlSubaie, R., Wee, R. W., Ritoux, A., Mishchanchuk, K., Passlack, J., Regester, D., & MacAskill, A. F. (2021). Control of parallel hippocampal output pathways by amygdalar long-range inhibition. _Elife_, _10_, e74758.
 

docs/source/tutorials/tracing-tracking.md

@@ -72,7 +72,7 @@ to find a mask that covers the axonal projections.
 Before we can proceed to register the axonal tracks in the imaged brain we need to install additional Napari plugins. 
 In this tutorial we will use the 
 [`napari-simpleitk-image-processing`](https://www.napari-hub.org/plugins/napari-simpleitk-image-processing) plugin. This 
-plugin can either be installed via the [napari plugin menu](https://napari.org/stable/plugins/find_and_install_plugin.html) 
+plugin can either be installed via the [napari plugin menu](https://napari.org/stable/plugins/start_using_plugins/finding_and_installing_plugins.html) 
 or directly from PyPI on the command-line:
 ```
 pip install napari-simpleitk-image-processing