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Add blackcap atlas paper #308

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Mar 11, 2025
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Add blackcap atlas paper #308

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3 changes: 2 additions & 1 deletion docs/source/projects/blackcap/index.md
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Expand Up @@ -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)
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4 changes: 4 additions & 0 deletions docs/source/publications.md
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# 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. (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):**

> 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)
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