ImageJ and 3D Slicer : open source 2 / 3D morphometric software

Pye F, Raja Schoob NB, Shirley B, Kocsis Á, Hohmann N, Murdock DJ, Jarochowska E (2019)

Publication Language: English

Publication Type: Conference contribution, Abstract of lecture

Publication year: 2019

Publisher: PeerJ Preprints

Conference Proceedings Title: Open Data and Analysis: from morphology to evolutionary patterns

Event location: Munich DE

DOI: 10.7287/peerj.preprints.27998


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,m 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 3DSlicer which focuses on 3D informatics and visualisation. They are easily extensible using common programming languages, with 3DSlicer 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. 3DSlicer 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.

Authors with CRIS profile

How to cite


Pye, F., Raja Schoob, N.B., Shirley, B., Kocsis, Á., Hohmann, N., Murdock, D.J., & Jarochowska, E. (2019, October). ImageJ and 3D Slicer : open source 2 / 3D morphometric software. Paper presentation at Annual Meeting of the Paleontological Society (Paläontologische Gesellschaft) 2019, Munich, DE.


Pye, Fiona, et al. "ImageJ and 3D Slicer : open source 2 / 3D morphometric software." Presented at Annual Meeting of the Paleontological Society (Paläontologische Gesellschaft) 2019, Munich PeerJ Preprints, 2019.

BibTeX: Download