diff --git a/docs/source/blog/ccfv2-atlases-added.md b/docs/source/blog/ccfv2-atlases-added.md new file mode 100644 index 00000000..f84d7ead --- /dev/null +++ b/docs/source/blog/ccfv2-atlases-added.md @@ -0,0 +1,50 @@ +--- +blogpost: true +date: April 29, 2026 +author: Jung Woo Kim +location: London, England +category: brainglobe +language: English +--- + +# Three Atlases for the Allen Common Coordinate Framework v2 Mouse Brain have been added to BrainGlobe + +The mouse brain atlases provided by the Allen Institute for Brain Science (AIBS) are widely used in the neuroscience community, and as of the writing of this blog post, the most updated version of their atlas uses version 3 of the Common Coordinate Framework (CCF). However, there are many benefits from adding older versions of atlases, namely in terms of keeping a record of the history of atlas versions, as well as reproducing historical results which used older atlases. Therefore, we have packaged the CCFv2 mouse brain atlase provided by the Allen Institute. This atlas comes with three sets of segmentations, one for the adult mouse, a more detailed set for the fiber tracts, and one based on developmental origin. The CCFv2 is a symmetric atlas constructed from the same 528 Nissl stained 25um coronal slices as in CCFv1, but reprocessed for symmetry and to introduce more annotations from the Allen Reference Atlas. + +We have packaged the following three atlases: +### 1. CCFv2 Mouse Brain Atlas +ccfv2 mouse brain atlas annotations + +**Figure 1. Anterior view of the CCFv2 Mouse Brain atlas annotations and reference image.** + +### 2. CCFv2 Mouse Fiber Tracts Atlas +ccfv2 mouse fiber tracts atlas annotations + +**Figure 2. Anterior view of the CCFv2 Mouse Fiber Tracts atlas annotations and reference image.** + +### 3. CCFv2 Developmental Mouse Brain Atlas +ccfv2 developmental mouse brain atlas annotations + +**Figure 3. Anterior view of the CCFv2 Developmental Mouse Brain atlas annotations and reference image.** + + +The BrainGlobe team re-packaged the data generated and made public by the Allen Institute, making it now possible to use the CCFv2 mouse atlases within the BrainGlobe ecosystem. The atlas names are `ccfv2_mouse_25um`, `ccfv2_fiber_mouse_25um`, and `ccfv2_dev_mouse_25um`. + +## How do I use the new atlases? + +You can use the CCFv2 atlases for visualisation like other BrainGlobe atlases, as written below: + +* Install BrainGlobe ([instructions](/documentation/index)) +* Open napari and follow the steps in our [download tutorial](/tutorials/manage-atlases-in-GUI.md) for the CCFv2 atlas +* Visualise the different parts of the atlas as described in our [visualisation tutorial](/tutorials/visualise-atlas-napari) + +The end result will look something like Figure 4. + +![ccfv2 mouse brain atlas visualised in napari](./images/ccfv2_mouse_brain_napari.png) + +**Figure 4: The CCFv2 Mouse Brain atlas visualised with `brainrender-napari`: with mesh overlays for the brain (grey), the hippocampal formation (green) and the cerebellum (yellow).** + +Additionally, the CCFv2 mouse brain atlas can be used in conjunction with our CCF Translator to translate data between other mouse brain atlases based on the CCFv2 framwework. For more details, check out the [CCF Translator GitHub page](https://github.com/brainglobe/brainglobe-ccf-translator). +## Why are we adding new atlases? + +A fundamental aim of the BrainGlobe project is to make various brain atlases easily accessible by users across the globe. The CCFv2 Mouse Brain atlases allow for users to use historical versions of the Allen 3D atlases easily on BrainGlobe. If you would like to get involved with a similar project, please [get in touch](/contact). diff --git a/docs/source/blog/images/ccfv2_dev_mouse.png b/docs/source/blog/images/ccfv2_dev_mouse.png new file mode 100644 index 00000000..098cb0f4 Binary files /dev/null and b/docs/source/blog/images/ccfv2_dev_mouse.png differ diff --git a/docs/source/blog/images/ccfv2_fiber_mouse.png b/docs/source/blog/images/ccfv2_fiber_mouse.png new file mode 100644 index 00000000..7f217c06 Binary files /dev/null and b/docs/source/blog/images/ccfv2_fiber_mouse.png differ diff --git a/docs/source/blog/images/ccfv2_mouse_brain.png b/docs/source/blog/images/ccfv2_mouse_brain.png new file mode 100644 index 00000000..6230b2be Binary files /dev/null and b/docs/source/blog/images/ccfv2_mouse_brain.png differ diff --git a/docs/source/blog/images/ccfv2_mouse_brain_napari.png b/docs/source/blog/images/ccfv2_mouse_brain_napari.png new file mode 100644 index 00000000..a417b591 Binary files /dev/null and b/docs/source/blog/images/ccfv2_mouse_brain_napari.png differ diff --git a/docs/source/documentation/brainglobe-atlasapi/_atlas_table.md b/docs/source/documentation/brainglobe-atlasapi/_atlas_table.md index 0b517913..d5b8ac7d 100644 --- a/docs/source/documentation/brainglobe-atlasapi/_atlas_table.md +++ b/docs/source/documentation/brainglobe-atlasapi/_atlas_table.md @@ -5,11 +5,11 @@ | [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) | 1 micron | 6 dpf | FISH | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#max-planck-zebrafish-brain-atlas) | | [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) | 10, 25, 50, and 100 micron | P56 | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#enhanced-and-unified-mouse-brain-atlas) | | [Enhanced and Unified Mouse Brain Atlas v2](https://figshare.com/articles/dataset/Unified_mouse_brain_atlas_v2/25750983) | 20 micron | P56 | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#enhanced-and-unified-mouse-brain-atlas-v2) | -| [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) | 10, 25, 50 and 100 micron | P56 | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#smoothed-version-of-the-kim-et-al-mouse-reference-atlas) | -| [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) | 20 micron | 8 to 10 weeks post natal | LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#gubras-lsfm-mouse-brain-atlas) | -| [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) | 20 x 10 x 10 micron | Adult | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#d-version-of-the-allen-mouse-spinal-cord-atlas) | +| [Smoothed version of the Kim et al. Mouse Reference Atlas](https://doi.org/10.1016/j.celrep.2014.12.014) | 10, 25, 50 and 100 micron | P56 | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#smoothed-version-of-the-kim-et-al-mouse-reference-atlas) | +| [Gubra's LSFM Mouse Brain Atlas](https://doi.org/10.1007/s12021-020-09490-8) | 20 micron | 8 to 10 weeks post natal | LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#gubras-lsfm-mouse-brain-atlas) | +| [3D version of the Allen Mouse Spinal Cord Atlas](https://doi.org/10.1101/2021.05.06.443008) | 20 x 10 x 10 micron | Adult | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#d-version-of-the-allen-mouse-spinal-cord-atlas) | | [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) | 4 micron | 15-16 weeks post natal | LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#azba-a-3d-adult-zebrafish-brain-atlas) | -| [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3) | 39 micron | P80 | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#waxholm-space-atlas-of-the-sprague-dawley-rat-brain) | +| [Waxholm Space Atlas of the Sprague Dawley Rat Brain](https://doi.org/10.1038/s41592-023-02034-3) | 39 micron | P80 | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#waxholm-space-atlas-of-the-sprague-dawley-rat-brain) | | [SWC Female Rat Brain Atlas](https://brainglobe.info/blog/swc-female-rat-atlas.html#native-female-rat-atlas) | 50 micron | 5–8 weeks old females | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#swc-female-rat-brain-atlas) | | [Waxholm-aligned SWC Female Rat Atlas](https://brainglobe.info/blog/swc-female-rat-atlas.html#waxholm-space-registered-female-rat-atlas) | 39 micron | 5–8 weeks old females (registered to Waxholm Space) | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#waxholm-aligned-swc-female-rat-atlas) | | [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) | 16, 16.75, and 25 micron | E13, E15, E18, P4, P14, P28 & P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#d-edge-aware-refined-atlases-derived-from-the-allen-developing-mouse-brain-atlases) | @@ -20,16 +20,19 @@ | [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) | 10 and 25 micron | P56 | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#bluebrain-barrel-cortex-atlas) | | [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3) | 40 micron | ~ 3 months post hatching | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#unam-axolotl-brain-atlas) | | [Prairie Vole Brain Atlas](https://doi.org/10.7554/eLife.87029.3.sa0) | 25 micron | Unknown | LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#prairie-vole-brain-atlas) | -| [Gubra's stereotaxic MRI mouse brain atlas](https://doi.org/10.1007/s12021-023-09623-9) | 25 micron | 10 week old | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#gubras-mri-mouse-brain-atlas) | -| [Gubra's LSFM mouse brain atlas v2](https://doi.org/10.1007/s12021-023-09623-9) | 25 micron | 10 week old | LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#gubras-lsfm-mouse-brain-atlas-v2) | -| [MRI mouse lemur brain atlas](https://doi.org/10.1016/j.dib.2018.10.067) | 91 micron | 15–58 months | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#mri-mouse-lemur-brain-atlas) | +| [Gubra's Stereotaxic MRI Mouse Brain Atlas](https://doi.org/10.1007/s12021-023-09623-9) | 25 micron | 10 week old | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#gubras-mri-mouse-brain-atlas) | +| [Gubra's LSFM Mouse Brain Atlas v2](https://doi.org/10.1007/s12021-023-09623-9) | 25 micron | 10 week old | LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#gubras-lsfm-mouse-brain-atlas-v2) | +| [MRI Mouse Lemur Brain Atlas](https://doi.org/10.1016/j.dib.2018.10.067) | 91 micron | 15–58 months | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#mri-mouse-lemur-brain-atlas) | | [Australian Mouse Brain Atlas](https://doi.org/10.1016/j.ymeth.2015.01.005) | 15 micron | 12 week old | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#australian-mouse-brain-atlas) | -| [Cat brain atlas](https://doi.org/10.1002/cne.24271) | 500 micron | Adult | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#cat-brain-atlas) | -| [Eurasian blackcap atlas](https://doi.org/10.1101/2025.03.04.641293) | 25 micron| Adult | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#eurasian-blackcap-atlas) | | +| [Cat Brain Atlas](https://doi.org/10.1002/cne.24271) | 500 micron | Adult | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#cat-brain-atlas) | +| [Eurasian Blackcap Atlas](https://doi.org/10.1101/2025.03.04.641293) | 25 micron| Adult | STPT | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#eurasian-blackcap-atlas) | | | [BlueBrain CCFv3 Augmented](https://doi.org/10.1162/imag_a_00565) | 10 and 25 micron | P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#ccfv3-augmented-mouse-atlas) | -| [Columbia cuttlefish atlas](https://doi.org/10.1016/j.cub.2023.06.007) | 50 micron | 6-7 months | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#columbia-cuttlefish-atlas) | +| [Columbia Cuttlefish Atlas](https://doi.org/10.1016/j.cub.2023.06.007) | 50 micron | 6-7 months | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#columbia-cuttlefish-atlas) | | [Kocher Bumblebee Brain Atlas](https://doi.org/10.1016/j.cub.2022.04.066) | 2.542 x 1.2407 x 1.2407 micron | Adult Worker | Confocal | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#kocher-bumblebee-brain-atlas) | -| Drosophila wing disc instar3 atlas| 2 micron | 3rd Instar Larvae | Confocal | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#Drosophila-wing-disc-instar3-atlas) | +| Drosophila Wing Disc instar3 Atlas| 2 micron | 3rd Instar Larvae | Confocal | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#Drosophila-wing-disc-instar3-atlas) | | [DeMBA Developmental Mouse Brain Atlas](https://doi.org/10.1038/s41467-025-63177-9) | 10, 20, and 25 micron | every day from P04 to P56 | MRI, STPT, LSFM | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#demba-developmental-mouse-brain-atlas) | -| [Dorr MRI Mouse Atlas](https://doi.org/10.1016/j.neuroimage.2008.03.037) | 32 micron | 12 week old | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#dorr-mri-mouse-atlas) | -| [CArea Mouse Atlas](https://doi.org/10.64898/2026.01.20.700446 ) | 25 micron | P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#carea-mouse-atlas) +| [Dorr MRI Mouse Atlas](https://doi.org/10.1016/j.neuroimage.2008.03.037) | 32 micron | 12 week old | MRI | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#dorr-mri-mouse-atlas) | +| [CArea Mouse Atlas](https://doi.org/10.64898/2026.01.20.700446 ) | 25 micron | P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#carea-mouse-atlas) | +| [Allen CCFv2 Mouse Brain Atlas](https://doi.org/10.1038/nature13186) | 25 micron | P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#ccfv2-mouse-brain-atlas) | +| [Allen CCFv2 Mouse Fiber Tracts Atlas](https://doi.org/10.1038/nature13186) | 25 micron | P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#ccfv2-mouse-fiber-atlas) | +| [Allen CCFv2 Developmental Mouse Brain Atlas](https://doi.org/10.1038/nature13186) | 25 micron | P56 | Nissl | [![More info](https://img.shields.io/badge/More%20info-Click%20here-blue)](https://brainglobe.info/documentation/brainglobe-atlasapi/usage/atlas-details.html#ccfv2-dev-mouse-atlas) | diff --git a/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md b/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md index 26488f33..6e606776 100644 --- a/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md +++ b/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md @@ -412,6 +412,38 @@ with some improvements. This atlas was constructed from reregistered ISH data fr Available versions: * `carea_mouse_25um` + +### [Allen CCFv2 Mouse Brain Atlas](https://doi.org/10.1038/nature13186) +This is a mouse brain atlas using version 2 of the commonly used Allen Common Coordinate Framework, which is included +here for historical reasons. The template is based on 528 Nissl-stained coronal slices from the mouse specimen used in +the Allen Reference Atlas. This atlas annotates the grey matter and ventricular systems of the mouse brain. Though it +is not without its faults (misalignment of coronal slices on the anterio-posterior axis), it still serves the very useful +purpose of providing a common coordinate framework for many other useful mouse atlases, which can be translated to other +atlases using the [BrainGlobe CCF Translator](https://github.com/brainglobe/brainglobe-ccf-translator). +This atlas was packaged from archived data from the Allen Institute for Brain Science. + +Available versions: +* `ccfv2_mouse_25um` + +### [Allen CCFv2 Mouse Fiber Tracts Atlas](https://doi.org/10.1038/nature13186) +This is a mouse brain fiber tract atlas using version 2 of the commonly used Allen Common Coordinate Framework. Where +the CCFv2 Mouse Brain atlas only provides information on the grey matter and ventricular systems of the mouse brain, +this atlas contains fiber tract structural annotation information. as delineated in the Allen Reference Atlas. The +template is based on 528 Nissl-stained coronal slices from the mouse specimen used in the Allen Reference Atlas. +This atlas was packaged from archived data from the Allen Institute for Brain Science. + +Available versions: +* `ccfv2_fiber_mouse_25um` + +### [Allen CCFv2 Developmental Mouse Brain Atlas](https://doi.org/10.1038/nature13186) +This is a developmental mouse brain atlas using version 2 of the commonly used Allen Common Coordinate Framework. +The template is based on 528 Nissl-stained coronal slices from the mouse specimen used in the Allen Reference Atlas. +The annotations contain the developmental taxonomy of mouse brain structures as given in the Allen Developing Mouse +Brain atlas. This atlas was packaged from archived data from the Allen Institute for Brain Science. + +Available versions: +* `ccfv2_dev_mouse_25um` + ## Rat ### [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3) The Waxholm Space rat brain atlas features annotations of 222 structures, alongside a 39μm MRI template. It provides detailed delineations