A reproducible and comprehensive workflow for growth stage-specific segmentation of X-ray µCT scan data of foraminifera

This dataset accompanies the publication with the same title in Marine Micropaleontology. Label data is available in two file formats; RAW (raw binary, little endian) and MSD (Microfossil Segmentation Data, readable in the MFSE toolbox and MATLAB). Label descriptions for the RAW files are supplied in TXT format. The RAW files are named the pattern used in Siccha et al. (2023) with the addition of a two-character descriptor after the specimen's name and the dimensional information, as below: L1 = all layer 1 labels; in situ chamber lumina and primary chamber shell wall labelsL2 = all layer 2 labels; in vivo chamber lumina and complete chamber shell wall labelsL3 = all layer 3 labels; shell derived chamber lumina and the original shell label Example explanation of file naming pattern:The file "GE_GRUA_1 L2 [365x384x331 - 1.2986 um - uchar]" contains the raw data of the scan no. 1 of Globigerinoides ruber albus, family Globigerinoidae, as a stream of 46,392,960 unsigned 8-Bit integers, without any file header, that need to be read into an array with a size of 365 by 384 by 331 elements in order to access the labels of the in vivo chamber lumina and complete chamber shell wall labels as voxels in 1.2986 µm cubic resolution. Example workflow for importing above file into ITK-Snap (Yushkevich et al., 2006):Retrieve the CT data raw data files for the specimen "GE_GRUA_1" from Siccha et al. (2023)Open Main Image / Select the respective raw data file and file type / Enter the required dimensional and data format information as given in the file name "GE_GRUA_1 [365x384x331 - 1.2986 um - uchar]".Open Segmentation / Select the label raw data file supplied with this publication "GE_GRUA_1 L2 [365x384x331 - 1.2986 um - uchar]" and file type / Enter the required dimensional and data format information as given in the file name / Refer to the TXT file "GE_GRUA_1 labeltable.txt" to identify the labels Example workflow for importing above file into MFSE (Siccha and Schmidt, 2026):Install the MFSE toolbox (Siccha 2026) / Load the respective MSD file via File / Load project References: Siccha, M., Schmidt, D., 2026. MFSE: A software toolbox for the segmentation and morphometric analysis of foraminifera µCT data. J. Open Res. Softw. 14: 42. https://doi.org/10.5334/jors.662 Siccha, M., Morard, R., Meilland, J., Iwasaki, S., Kucera, M., Kimoto, K., 2023. Collection of X-ray micro computed tomography images of shells of planktic foraminifera with curated taxonomy. Sci. Data 10, 679. https://doi.org/10.1038/s41597-023-02498-0 Yushkevich, P.A., Piven, J., Hazlett, H.C., Smith, R.G., Ho, S., Gee, J.C., Gerig, G., 2006. User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. NeuroImage 31, 1116–1128. https://doi.org/10.1016/j.neuroimage.2006.01.015