From ee15990cd3b122a21297e212fc0f8bbb603e705a Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Thu, 12 Sep 2024 11:07:48 +0100 Subject: [PATCH] Improve atlas details within atlas API docs (#249) --- .github/workflows/docs_build_and_deploy.yml | 2 +- .../usage/atlas-details.md | 28 +++++++++++++++++-- docs/source/publications.md | 8 ++---- docs/source/tutorials/tracing-tracking.md | 2 +- 4 files changed, 30 insertions(+), 10 deletions(-) diff --git a/.github/workflows/docs_build_and_deploy.yml b/.github/workflows/docs_build_and_deploy.yml index 287bbfc0..b9dca4fd 100644 --- a/.github/workflows/docs_build_and_deploy.yml +++ b/.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 diff --git a/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md b/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md index a283eff9..75ba8b3f 100644 --- a/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md +++ b/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. diff --git a/docs/source/publications.md b/docs/source/publications.md index 021f4f22..3ef1a180 100644 --- a/docs/source/publications.md +++ b/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)). 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)). 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. diff --git a/docs/source/tutorials/tracing-tracking.md b/docs/source/tutorials/tracing-tracking.md index 71314785..cef0b2a1 100644 --- a/docs/source/tutorials/tracing-tracking.md +++ b/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