Manuscript Title

David Haberthür; Pui Ching Chu; Larisa Petra Kaija

Manuscript Title

This manuscript (permalink) was automatically generated from habi/InMiceMethodPaper@46eb2e1 on August 18, 2025.

Authors

David Haberthür
0000-0003-3388-9187 · habi · @habi@mastodon.social
Institute of Anatomy, University of Bern, Baltzerstrasse 2, 3012 Bern, Switzerland
Pui Ching Chu
0009-0006-5408-300X · puipuichu
Animal Welfare Division, Veterinary Public Health Institute, University of Bern, Länggassstrasse 120, CH-3012 Bern, Switzerland · Funded by Swiss National Science Foundation (SNSF) (Grant 310030_219196)
Larisa Petra Kaija
0009-0001-1871-5915 · LarisaKaija
Animal Welfare Division, Veterinary Public Health Institute, University of Bern, Länggassstrasse 120, 3012 Bern, Switzerland

✉ — Correspondence possible via GitHub Issues

Abstract

Background & Summary

We scanned a lot of different mouse strains and so-called hybrids, both male and female. One scan for each strain, each hybrid and each sex gives already 90 samples.

Methods

Sample preparation

Mice were anesthesized
Mice were decapitated
Mouse skulls were stored in …

Tomographic imaging

SkyScan 1272 with sample changer
All log files available here: https://github.unibe.ch/david-haberthuer/InMice/tree/main/logfiles
Report scaning settings and reconstruction parameter data according to¹

Image processing

Jupyter² notebooks, available here: https://github.unibe.ch/david-haberthuer/InMice/, for reproducible research.

Data Records

Technical Validation

Usage Notes

Code Availability

Jupyter notebooks

References

Stock, S. R. & De Carlo, F. Meta-data for absorption tomography measurements. Tomography of Materials and Structures 3, 100015 (2023).

Kluyver, T. et al. Jupyter Notebooks – a publishing format for reproducible computational workflows. in (eds. Loizides, F. & Scmidt, B.) 87–90 (IOS Press, 2016). doi:10.3233/978-1-61499-649-1-87.

ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy. doi:10.3789/ansi.niso.z39.104-2022.

Himmelstein, D. S. et al. Open collaborative writing with Manubot. PLoS Comput Biol 15, e1007128 (2019).

Author Contributions

Contributor Roles Taxonomy (CRediT), as defined in³:

Data curation: David Haberthür, Larisa Petra Kaija
Formal analysis: David Haberthür
Investigation: David Haberthür, Pui Ching Chu, Larisa Petra Kaija
Methodology: David Haberthür, Pui Ching Chu, Larisa Petra Kaija
Project administration: David Haberthür, Pui Ching Chu
Resources: Pui Ching Chu
Software: David Haberthür
Validation: David Haberthür, Pui Ching Chu, Larisa Petra Kaija
Visualization: David Haberthür
Writing – original draft: David Haberthür
Writing – review & editing: David Haberthür, Pui Ching Chu, Larisa Petra Kaija

Competing Interests

Author	Competing Interests	Last Reviewed
David Haberthür	None	2025-06-27
Pui Ching Chu	None	2025-06-27
Larisa Petra Kaija	None

Acknowledgements

We are grateful to the Microscopy Imaging Center of the University of Bern for their infrastructural support. We also thank the manubot project⁴ for facilitating collaborative writing of this manuscript.