From 3daf99b47100bd3f24093474ed060111f19a11e4 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 11 Mar 2025 11:08:12 +0000 Subject: [PATCH 1/3] Add blackcap atlas paper --- docs/source/projects/blackcap/index.md | 3 ++- docs/source/publications.md | 4 ++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/source/projects/blackcap/index.md b/docs/source/projects/blackcap/index.md index 6b067c46..ec83ade0 100644 --- a/docs/source/projects/blackcap/index.md +++ b/docs/source/projects/blackcap/index.md @@ -18,7 +18,8 @@ For this reason, we collaborated with [Simon Weiler](https://sites.google.com/vi of the blackcap brain. ## Process -Full details of the atlas generation process are available in the preprint, however it is briefly as follows: +Full details of the atlas generation process are available in the [preprint](https://doi.org/10.1101/2025.03.04.641293 ), +however it is briefly as follows: 1. Acquire high-resolution whole-brain images using the [Sainsbury Wellcome Centre serial section two-photon platform](https://swcmicroscopy.com) 2. Crop images to generate individual hemisphere images without damage (we used 18 hemispheres from 10 birds) diff --git a/docs/source/publications.md b/docs/source/publications.md index 4951a9af..de226321 100644 --- a/docs/source/publications.md +++ b/docs/source/publications.md @@ -1,5 +1,9 @@ # BrainGlobe publications +- **Eurasian blackcap (_Sylvia atricapilla_) atlas:** + + > Sirmpilatze, N., Felder, A., Abdulazhanova, D., Schwigon, L., Haase, K., Musielak, I., Margrie, T. W., Mouritsen, H., Heyers, D., Tyson, A. L. , Weiler, S. *bioRxiv* 2025.03.04.641293; doi: [doi.org/10.1101/2025.03.04.641293](https://doi.org/10.1101/2025.03.04.641293) + - **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) From 29edf5333855aea47199a06ab71082dfa9962441 Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 11 Mar 2025 11:14:34 +0000 Subject: [PATCH 2/3] Add date and title --- docs/source/publications.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/publications.md b/docs/source/publications.md index de226321..56379ae4 100644 --- a/docs/source/publications.md +++ b/docs/source/publications.md @@ -2,7 +2,7 @@ - **Eurasian blackcap (_Sylvia atricapilla_) atlas:** - > Sirmpilatze, N., Felder, A., Abdulazhanova, D., Schwigon, L., Haase, K., Musielak, I., Margrie, T. W., Mouritsen, H., Heyers, D., Tyson, A. L. , Weiler, S. *bioRxiv* 2025.03.04.641293; doi: [doi.org/10.1101/2025.03.04.641293](https://doi.org/10.1101/2025.03.04.641293) + > Sirmpilatze, N., Felder, A., Abdulazhanova, D., Schwigon, L., Haase, K., Musielak, I., Margrie, T. W., Mouritsen, H., Heyers, D., Tyson, A. L. , Weiler, S. (2025) "Mapping the magnetoreceptive brain: A 3D digital atlas of the migratory bird Eurasian blackcap (Sylvia atricapilla)" *bioRxiv* 2025.03.04.641293; doi: [doi.org/10.1101/2025.03.04.641293](https://doi.org/10.1101/2025.03.04.641293) - **Brainreg & brainglobe-segmentation (formerly brainreg-segment):** From b4cd5ab1c0b17fb8ac954bf88447f1587d1348cf Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Tue, 11 Mar 2025 13:10:09 +0000 Subject: [PATCH 3/3] Remove space --- docs/source/projects/blackcap/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/projects/blackcap/index.md b/docs/source/projects/blackcap/index.md index ec83ade0..c6e31c6e 100644 --- a/docs/source/projects/blackcap/index.md +++ b/docs/source/projects/blackcap/index.md @@ -18,7 +18,7 @@ For this reason, we collaborated with [Simon Weiler](https://sites.google.com/vi of the blackcap brain. ## Process -Full details of the atlas generation process are available in the [preprint](https://doi.org/10.1101/2025.03.04.641293 ), +Full details of the atlas generation process are available in the [preprint](https://doi.org/10.1101/2025.03.04.641293), however it is briefly as follows: 1. Acquire high-resolution whole-brain images using the [Sainsbury Wellcome Centre serial section two-photon platform](https://swcmicroscopy.com)