From ab6bea9ce574003ef2c2e95df11347e6d117e915 Mon Sep 17 00:00:00 2001 From: Harry Carey Date: Tue, 28 Apr 2026 15:05:00 +0100 Subject: [PATCH 1/9] Create the-mega-packaging-project.md --- docs/source/blog/the-mega-packaging-project.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/source/blog/the-mega-packaging-project.md diff --git a/docs/source/blog/the-mega-packaging-project.md b/docs/source/blog/the-mega-packaging-project.md new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/docs/source/blog/the-mega-packaging-project.md @@ -0,0 +1 @@ + From 7c41c2f2e0c61309f0389effce35cd695b3c4976 Mon Sep 17 00:00:00 2001 From: Harry Carey Date: Tue, 28 Apr 2026 15:58:30 +0100 Subject: [PATCH 2/9] Add blog post for the mega packaging project Added metadata and introductory content for the mega packaging project blog post, detailing the integration of 3D atlases into the BrainGlobe API. --- .../source/blog/the-mega-packaging-project.md | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/docs/source/blog/the-mega-packaging-project.md b/docs/source/blog/the-mega-packaging-project.md index 8b137891..ee8e37b9 100644 --- a/docs/source/blog/the-mega-packaging-project.md +++ b/docs/source/blog/the-mega-packaging-project.md @@ -1 +1,28 @@ +--- +blogpost: true +date: April 28, 2026 +author: Harry Carey +location: London, England +category: brainglobe +language: English +--- + +# The mega packaging project + +The purpose of the BrainGlobe atlas api has always been to standardise atlases and provide them to researchers via a common, easy to use, interface. As part of this initiative we have integrated atlases of all kinds, including atlases of bees, cuttlefish, mice, and more. The logical endpoint of all of this would be integrate _all_ existing 3D atlases into BrainGlobe. + +While this may be a long process we have decided to start. First by creating a comprehensive list of all published non-human brain atlases which is available [here](https://docs.google.com/spreadsheets/d/18_ow4llQQVuwKu5WWM3PsZ1SjmeNYAhi6eENzhQRc40/edit?usp=sharing). This list is a work in progress and if you find an atlas which is not mentioned please open an issue on the [brainglobe-atlasapi](https://github.com/brainglobe/brainglobe-atlasapi/issues?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen) repository and we will be sure to add it. + +The second step is to actually integrate the atlases on this list into the API. To this end we have hired [Jung Woo Kim](https://github.com/kjungwoo5) and [Amirreza Bahramani](https://github.com/bahramani). They have already begun integrating several atlases (expect to see a Macaque atlas soon!). + +In total our review found 221 3D atlases across approximately 89 species of which we could find shared data for 121. + +```{figure} ../_static/atlases.png +:alt: BrainGlobe Atlases +:width: 65% +:align: center +:name: fig-bg-atlases + +Figure 1. The BrainGlobe ecosystem provides a common interface for a wide range of neuroanatomical atlases across species. +``` From 25aefa0483a5f669c14a94e9860efa90462b2bb6 Mon Sep 17 00:00:00 2001 From: Harry Carey Date: Tue, 28 Apr 2026 15:59:01 +0100 Subject: [PATCH 3/9] add bubble chart for blog post --- docs/source/_static/species_bubbles.svg | 3744 +++++++++++++++++++++++ 1 file changed, 3744 insertions(+) create mode 100644 docs/source/_static/species_bubbles.svg diff --git a/docs/source/_static/species_bubbles.svg b/docs/source/_static/species_bubbles.svg new file mode 100644 index 00000000..30b1828d --- /dev/null +++ b/docs/source/_static/species_bubbles.svg @@ -0,0 +1,3744 @@ + + + + + + + + 2026-04-28T15:57:23.430668 + image/svg+xml + + + Matplotlib v3.7.1, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 58504955ffab0fa2245c65e18a4f20358bd596e2 Mon Sep 17 00:00:00 2001 From: Harry Carey Date: Tue, 28 Apr 2026 16:29:42 +0100 Subject: [PATCH 4/9] add interacctive bubble chart --- docs/source/_static/species_bubbles.html | 34 ++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 docs/source/_static/species_bubbles.html diff --git a/docs/source/_static/species_bubbles.html b/docs/source/_static/species_bubbles.html new file mode 100644 index 00000000..f8b044b1 --- /dev/null +++ b/docs/source/_static/species_bubbles.html @@ -0,0 +1,34 @@ + + + +
+
+ + \ No newline at end of file From 43e8bb24c7aeda446665715059cfe9e3cc2c4181 Mon Sep 17 00:00:00 2001 From: Harry Carey Date: Tue, 28 Apr 2026 16:38:59 +0100 Subject: [PATCH 5/9] Update visualization and contribution information Replaced the BrainGlobe atlases figure with an iframe for species bubbles visualization and updated the contribution section. --- docs/source/blog/the-mega-packaging-project.md | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/docs/source/blog/the-mega-packaging-project.md b/docs/source/blog/the-mega-packaging-project.md index ee8e37b9..820d34de 100644 --- a/docs/source/blog/the-mega-packaging-project.md +++ b/docs/source/blog/the-mega-packaging-project.md @@ -17,12 +17,15 @@ The second step is to actually integrate the atlases on this list into the API. In total our review found 221 3D atlases across approximately 89 species of which we could find shared data for 121. -```{figure} ../_static/atlases.png -:alt: BrainGlobe Atlases -:width: 65% -:align: center -:name: fig-bg-atlases - -Figure 1. The BrainGlobe ecosystem provides a common interface for a wide range of neuroanatomical atlases across species. +```{raw} html + ``` +As always, if you would like to get involved with this project just get in touch with us! There are several ways to contribute including adding missing atlases to the list, helping with data standardisation, or contributing to integration and validationWe are available via GitHub issues and [zulip](https://brainglobe.zulipchat.com). + From 8fda8e4ec10ddedd3a48996fa181248bafcf1778 Mon Sep 17 00:00:00 2001 From: Harry Carey Date: Tue, 28 Apr 2026 16:39:54 +0100 Subject: [PATCH 6/9] Delete docs/source/_static/species_bubbles.svg --- docs/source/_static/species_bubbles.svg | 3744 ----------------------- 1 file changed, 3744 deletions(-) delete mode 100644 docs/source/_static/species_bubbles.svg diff --git a/docs/source/_static/species_bubbles.svg b/docs/source/_static/species_bubbles.svg deleted file mode 100644 index 30b1828d..00000000 --- a/docs/source/_static/species_bubbles.svg +++ /dev/null @@ -1,3744 +0,0 @@ - - - - - - - - 2026-04-28T15:57:23.430668 - image/svg+xml - - - Matplotlib v3.7.1, https://matplotlib.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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