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title: 'BoneJ Headless: Automated Software for Skeletal Microstructure Analysis'

tags:

  • Python
  • Fiji
  • ImageJ
  • microstructure metrics
  • microarchitecture metrics
  • bone
  • trabecular bone

authors:

  • name: Harsha Marupudi orcid: 0000-0002-6287-2387 equal-contrib: true affiliation: "Food and Drug Administration"
  • name: Author Without ORCID equal-contrib: true # (This is how you can denote equal contributions between multiple authors) affiliation: 2
  • name: Author with no affiliation corresponding: true # (This is how to denote the corresponding author) affiliation: 3 affiliations:
  • name: Lyman Spitzer, Jr. Fellow, Princeton University, USA index: 1
  • name: Institution Name, Country index: 2
  • name: Independent Researcher, Country index: 3 date: 13 August 2017 bibliography: paper.bib

Optional fields if submitting to a AAS journal too, see this blog post:

https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing

aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. aas-journal: Astrophysical Journal <- The name of the AAS journal.

Summary

Statement of need

Mathematics

Citations

Citations to entries in paper.bib should be in rMarkdown format.

If you want to cite a software repository URL (e.g. something on GitHub without a preferred citation) then you can do it with the example BibTeX entry below for @fidgit.

For a quick reference, the following citation commands can be used:

  • @author:2001 -> "Author et al. (2001)"
  • [@author:2001] -> "(Author et al., 2001)"
  • [@author1:2001; @author2:2001] -> "(Author1 et al., 2001; Author2 et al., 2002)"

Figures

Figures can be included like this: Caption for example figure.\label{fig:example} and referenced from text using \autoref{fig:example}.

Figure sizes can be customized by adding an optional second parameter: Caption for example figure.{ width=20% }

Acknowledgements

We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong Oh, and support from Kathryn Johnston during the genesis of this project.

References

Example paper.bib file:

@article{Pearson:2017, url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P}, Archiveprefix = {arXiv}, Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.}, Eprint = {1703.04627}, Journal = {ArXiv e-prints}, Keywords = {Astrophysics - Astrophysics of Galaxies}, Month = mar, Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}}, Year = 2017 }

@book{Binney:2008, url = {http://adsabs.harvard.edu/abs/2008gady.book.....B}, Author = {{Binney}, J. and {Tremaine}, S.}, Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.}, Publisher = {Princeton University Press}, Title = {{Galactic Dynamics: Second Edition}}, Year = 2008 }

@article{gaia, author = {{Gaia Collaboration}}, title = "{The Gaia mission}", journal = {Astronomy and Astrophysics}, archivePrefix = "arXiv", eprint = {1609.04153}, primaryClass = "astro-ph.IM", keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes}, year = 2016, month = nov, volume = 595, doi = {10.1051/0004-6361/201629272}, url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G}, }

@article{astropy, author = {{Astropy Collaboration}}, title = "{Astropy: A community Python package for astronomy}", journal = {Astronomy and Astrophysics}, archivePrefix = "arXiv", eprint = {1307.6212}, primaryClass = "astro-ph.IM", keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools}, year = 2013, month = oct, volume = 558, doi = {10.1051/0004-6361/201322068}, url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A} }

@misc{fidgit, author = {A. M. Smith and K. Thaney and M. Hahnel}, title = {Fidgit: An ungodly union of GitHub and Figshare}, year = {2020}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/arfon/fidgit}