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3D Cybertype datasets for: Pheidole klaman sp. N.: A new addition from Ivory Coast to the Afrotropical pulchella species group (Hymenoptera, Formicidae, Myrmicinae)

Citation

Hita Garcia, Francisco; Katzke, Julian; Economo, Evan P. (2022), 3D Cybertype datasets for: Pheidole klaman sp. N.: A new addition from Ivory Coast to the Afrotropical pulchella species group (Hymenoptera, Formicidae, Myrmicinae), Dryad, Dataset, https://doi.org/10.5061/dryad.mpg4f4r1k

Abstract

In this study we update the taxonomy of the Pheidole pulchella species group for the Afrotropical region and we describe the new species P. klaman sp. nov. We integrate the new species into the existing taxonomic system by providing an updated identification key for the whole group and updating the known distribution ranges of its members. We provide high quality focus stacking images, along with X–ray micro–CT scanned digital 3D representations, of major and minor worker type specimens. The Cybertype dataset provided in this study consist of the full micro-CT original volumetric datasets (in DICOM format), 3D surface models (in PLY formats), 3D rotation video files (in MP4 format), all stacked digital color images, and all image plates including all important images of 3D models for each species. In addition to the cybertype data at Dryad, we also provide freely accessible 3D surface models of all treated species on Sketchfab (holotype: https://skfb.ly/o68Qw; paratypes: https://skfb.ly/o68Qq & https://skfb.ly/o68Qo).

Methods

Specimens were examined under a Leica MZ16A stereo microscope and measured at x100. All images have been modified from originals and edited using GIMP (to compose the figures), IMAGEJ (to scale and add scale bars) and Polarr Photo Editor freeware (to sharpen, improve exposure and contrast). All micro-CT scans were performed at the Okinawa Institute of Science and Technology Graduate University (OIST), Japan, using a Zeiss Xradia 510 Versa 3D X-ray microscope operated with the Zeiss Scout-and-Scan Control System software (version 11.1.6411.17883) and saved in DICOM format. 3D reconstructions of the resulting scan projection data were done with the Zeiss Scout-and-Scan Control System Reconstructor (version 11.1.6411.17883) and saved in DICOM file format. Postprocessing of DICOM raw data was performed with Amira software (version 6.3). Virtual examinations of 3D surface models were performed by using the ‘volren’ function. The desired volume renderings were generated by adjusting colour space range to a minimum so that the exterior surface of specimens remained visible at the highest available quality. The 3D models were rotated and manipulated to allow a complete virtual examination of the scanned specimens in Amira, and in addition, exported in PLY format to be uploaded to the online 3D model platform Sketchfab (https://sketchfab.com).

Images of shaded surface display volume renderings were made with the ‘snapshot’ function at the highest achievable resolution (usually at around 1900 × 893 pixels). Surface rendering rotational videos were created in BLENDER (ver. 2.91, Blender Foundation, https://www.blender.org/). For optimal display, surface models exported from Amira were shaded ‘smooth’, scaled to about 1 m, illuminated with HDRI lighting, and rotated around their own z-axis based on specimens’ lateral views.All specimens used in this study have been databased, and the data are freely accessible on AntWeb (http://www.antweb.org). Each specimen can be traced by a unique specimen identifier attached to its pin (i.e., CASENT#, KGCOL#, XE#, being # a number).

Usage Notes

Summary of micro-CT scanning parameters with resulting voxel sizes (optical magnification was 4x and image size 1013x1013) for all three scanned specimens.

subcaste specimen ID magnification voxel size (μm) exposure (s) power (W) voltage (kV) Current (uA)
major CASENT0764691 4x 5.7854 1.2 5.92 70 85
minor CASENT0745509 4x 4.6952 0.6 4.01 50 80
minor CASENT0764692 4x 5.3599 0.6 6.02 70 85

Funding

Japan Society for the Promotion of Science, Award: 21K06326

Japan Society for the Promotion of Science, Award: 18K14768

Japan Society for the Promotion of Science, Award: 17K15180