MFSE (MicroFossil Segmentation Editor): A GUI for Editing 3D Segmentations of Foraminifera Derived from X-Ray µCT

Michael Siccha; Dave Schmidt

doi:10.5334/jors.662

MFSE (MicroFossil Segmentation Editor): A GUI for Editing 3D Segmentations of Foraminifera Derived from X-Ray µCT

Journal of Open Research Software

Volume 14 (2026): Issue 1

By: Michael Siccha and Dave Schmidt

Open Access

|Jun 2026

Abstract

X-ray microcomputed tomography (X-ray µCT) allows the quantification of morphological features of microfossils in an unprecedented level of detail and completeness. To support accurate and reproducible extraction of morphological data from scan datasets, we present a graphical user interface (GUI)-based software toolbox that facilitates comprehensive manipulation of microfossil segmentation data. Installation files are available on GitHub and Zenodo, and the source code is hosted on GitHub. Beyond its intended application to foraminifera, the software could be adapted for the manipulation of segmentation data of other polythalamous, interconnected biological structures.

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