ImageJ and 3D Slicer: open source 2/3D morphometric software
- Published
- Accepted
- Subject Areas
- Bioinformatics, Mathematical Biology, Paleontology
- Keywords
- morphometrics, palaeontology, image processing, fossil, shape analysis, bivalves, spherical harmonics, coniform, conodonts
- Copyright
- © 2019 Pye et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. ImageJ and 3D Slicer: open source 2/3D morphometric software. PeerJ Preprints 7:e27998v2 https://doi.org/10.7287/peerj.preprints.27998v2
Abstract
In a world where an increasing number of resources are hidden behind paywalls and monthly subscriptions, it is becoming crucial for the scientific community to invest energy into freely available, community-maintained systems. Open-source software projects offer a solution, with freely available code which users can utilise and modify, under an open source licence. In addition to software accessibility and methodological repeatability, this also enables and encourages the development of new tools.
As palaeontology moves towards data driven methodologies, it is becoming more important to acquire and provide high quality data through reproducible systematic procedures. Within the field of morphometrics, it is vital to adopt digital methods that help mitigate human bias from data collection. In addition, mathematically founded approaches can reduce subjective decisions which plague classical data. This can be further developed through automation, which increases the efficiency of data collection and analysis.
With these concepts in mind, we introduce two open-source shape analysis software, that arose from projects within the medical imaging field. These are ImageJ, an image processing program with batch processing features, and 3D Slicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3D Slicer containing an internal python interactor, and ImageJ allowing the incorporation of several programming languages within its interface alongside its own simplified macro language. Additional features created by other users are readily available, on GitHub or through the software itself.
In the examples presented, an ImageJ plugin “FossilJ” has been developed which provides semi-automated morphometric bivalve data collection. 3D Slicer is used with the extension SPHARM-PDM, applied to synchrotron scans of coniform conodonts for comparative morphometrics, for which small assistant tools have been created in Python.
Author Comment
This is a preprint submission to PeerJ Preprints.
Correction of author details and replaced figure.