Microcomputed tomography (µCT) of male and female adult quail skulls
Data files
Jul 24, 2026 version files 34.16 GB
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Quail_Adult_Female.zip
12.75 GB
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Quail_Adult_Male.zip
21.41 GB
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README.md
4.50 KB
Abstract
This dataset contains high-resolution microcomputed tomography (µCT) scans of male and female adult Japanese quail (Coturnix coturnix japonica) heads, which were collected to analyze three-dimensional (3D) craniofacial morphology, skull architecture, and potential sexual dimorphism while establishing a comprehensive anatomical baseline for avian developmental and evolutionary biology studies. The dataset includes standard DICOM image series (.dcm files) alongside native SCANCO Medical 3D volumetric reconstructions, featuring the master high-resolution grayscale datasets (.aim), their corresponding segmented/thresholded 3D structural models (_seg.aim), and the OpenVMS automated batch scripts (*.com) utilized for region-of-interest evaluation and DICOM image conversion.
Dataset DOI: 10.5061/dryad.v15dv42ch
Description of the data and file structure
These data were collected to analyze 3D craniofacial morphology, skeletal architecture, and potential sexual dimorphism in adult Japanese quail (Coturnix coturnix japonica) heads, while simultaneously establishing a comprehensive anatomical baseline for avian developmental and evolutionary biology studies. High-resolution micro-computed tomography (µCT) scans were utilized to capture precise 3D volumetric reconstructions and calibrated bone mineral density metrics across male and female specimens.
Files and variables
File: Quail_Adult_Female.zip
Description: Contains the complete dataset for the female specimen (ID: f0003041), consisting of 1,816 sequential DICOM slices and associated SCANCO processing files.
File: Quail_Adult_Male.zip
Description: Contains the complete dataset for the male specimen (ID: f0003042), consisting of 2,400 sequential DICOM slices and associated SCANCO processing files.
Individual files are prefixed with their respective system measurement identifiers (f0003041 for female, f0003042for male).
f[ID]_[00000-xxxxx].dcm: Standard 2D DICOM slice images representing sequential cross-sections of the reconstructed 3D skull anatomy.f[ID].aim: Native SCANCO Medical master 3D volumetric reconstruction dataset containing raw grayscale X-ray attenuation/density data and embedded scan metadata.f[ID]_seg.aim: Segmented (thresholded) binary 3D dataset generated by SCANCO software, isolating solid bone structures from background noise.f[ID]_eval_voi1.com: Automated OpenVMS plain-text script used natively by SCANCO software to execute the mathematical Volume of Interest (VOI) segmentation.f[ID]_eval_cvt_dicom.com: Automated OpenVMS plain-text script utilized by the SCANCO software to batch-convert and export the 3D volume into the 2D DICOM series.
Code/software
Software Requirements
No proprietary software is strictly required to view the primary data, as the dataset includes standardized DICOM files.
- For DICOM (
.dcm) Files: These can be opened natively in any free, open-source medical imaging software such as Fiji/ImageJ (all versions), 3D Slicer, or Horos/OsiriX. - For SCANCO (
.aim) Files: These raw 3D volumes can be imported into Fiji/ImageJ by installing the open-source Bio-Formats plugin (v5.0 or later). Alternatively, they can be processed programmatically using the open-source Python libraryaim2numpy.
Included Code and Scripts (.com files)
This submission includes automated batch scripts generated natively by the SCANCO Medical OpenVMS operating environment:
f[ID]_eval_voi1.com: A plain-text command script detailing the parameters used to isolate the 3D volume of interest (VOI) from the background scan.f[ID]_eval_cvt_dicom.com: A plain-text command script executing the automated slice extraction and conversion from the master.aimfile into the accompanying.dcmimage series.
Note: These .com files are provided for archival completeness and transparency regarding the SCANCO processing pipeline; they do not need to be executed by users to access the imaging data.
Data Workflow Relationship
f[ID].aimis the master 3D grid containing the raw density data.f[ID]_eval_voi1.comwas used to filter and isolate the skull tissue to generate the binarized bone model,f[ID]_seg.aim.f[ID]_eval_cvt_dicom.comwas executed to slice the 3D master volume into the independent 2D cross-sections (f[ID]_00000.dcmonward) for universal viewing.
Access information
Other publicly accessible locations of the data:
- None. This dataset is not currently hosted or publicly accessible on any other digital repository or repository mirrors.
Data were derived from the following sources:
- None. This is an original, primary dataset. The underlying physical specimens (adult Coturnix coturnix japonica heads) were obtained from AA Laboratory Eggs (Westminster, CA). All imaging data, reconstructions, and segmentations were generated directly by the author at the UCSF Skeletal Biology and Biomechanics Core. No parts of this data were derived from pre-existing third-party digital repositories or published datasets.
Frozen adult heads of male and female Japanese quail (Coturnix coturnix japonica) were obtained from AA Laboratory Eggs, Westminster, CA. Heads were formalin-fixed overnight, washed in 1X PBS, placed in 50 mL Falcon tubes, and scanned using a SCANCO μCT50 cone-beam µCT (Scanco Medical, Switzerland) at a resolution of 10 µm. All specimens were scanned using the same energy/intensity settings (55 kVp, 109 µA, 6 W), calibration settings (55 kVp, 0.5mm Al filter, beam hardening: 1200 mg HA/ccm) at the Skeletal Biology and Biomechanics Core, Core Center for Musculoskeletal Biology and Medicine, University of California, San Francisco (UCSF). Scans were reconstructed using the SCANCO Medical software, and all data slice sequences were converted into a standard DICOM image series using the built-in export function within the main SCANCO Evaluation/Visualization software package.