The present package is based on the long-bone-diaphyseal-CSG-Toolkit and has been created to simplify its installation and usage from within GNU Octave. It is based on novel and robust algorithms for calculating the cross-sectional geometric properties of the diaphyses of humerus, ulna, femur, and tibia bones represented as a triangular mesh in a Wavefront OBJ 3D model file format.
This package provides numerous functions for analyzing CSG properties and working with 3D models. You can find its documentation at https://pr0m1th3as.github.io/csg-toolkit/.
The CSG Toolkit is compatible with later versions of Octave >= v7.2.0 and depends
on the io >= 2.6.4 package.
To download and install the latest version (1.3.2), type:
pkg install -forge csg-toolkit
The package can be loaded on demand with the following commmand:
pkg load csg-toolkit
Happy long bone analysis!
The CSG Toolkit can be called in batch processing mode using the longbone_Analysis
function which can handle all available 3D models found in OBJ format in any chosen
directory. Batch processing is available for all three modes of Geometry:
- Default: utilizing the
longbone_Geometryfunction for analyzing cross sections at the standard 20%, 35%, 50%, 65%, and 80% intervals. - Custom: utilizing the
longbone_CustomGeomteryfunction for analyzing arbitrary cross sections at any user specified interval between 10% and 90%. - Fragment: utilizing the
longbone_FragmentGeometryfunction for analysing cross sections from arbitrary long bone fragments.
Although this functionality is still available, there is no longer need to work with a specific bone being present in a folder for batch proccessing. The user may select a specific bone, i.e. Humerus, or may choose to process different bones in a single batch process. Bone models that do not match the user selection are omitted from batch processing.
After batch processing, the function inspect_CSG can be used for visual inspection
of the calculated cross-sectional contours according to the CSV files present in the
working directory. Furthermore, it will assemble all calculated values from the
the samples (bones) that have been verified by the user and save them in a CSV file.
The need for MeshLab .pp side car files has been also relaxed. If they are present
along with their OBJ counterparts, they are utilized, if not, the initial alignment
points are automatically registered with the longbone_Registration function.
Moreover, the new function longbone_CustomGeometry allows for arbitrary user
defined cross sections along the longitudinal axis of the bones.
The CSG Toolkit also provides functionality for graphical representation of the
cross-sectional contours and their respective CSG properties, which can be ploted
with the visualize_CrossSections function, which utilizes the output results of
either longbone_Analysis stored in relevant CSV files, or the return structures
of the longbone_Geometry function and the generated CSV files from the
longbone_CustomGeometry function.
The latest release (1.3.2) introduced a GUI utility for biological sex estimation.
Type help estimate_sex to find out how to utilize CSG properties for biological
profiling from the long bones. More functionality comming soon!
If you find this package usefull for your research, please include the following citations:
Bertsatos A, Chovalopoulou M-E. 2019. A novel method for analyzing long bone diaphyseal cross-sectional geometry. A GNU Octave CSG Toolkit. Forensic Science International 297: 65–71. https://doi.org/10.1016/j.forsciint.2019.01.041
Bertsatos A, Garoufi N, Koliaraki M, Chovalopoulou M-E. 2023. Paving new ways in forensic contexts with virtual osteology applications: csg-toolkit – a 3D osteology package for cross-sectional geometry analysis. Annals of 3D Printed Medicine, 9, 100094. https://doi.org/10.1016/j.stlm.2022.100094
The present toolkit has been extensively tested and these results are presented in the relevant validation study available at https://doi.org/10.5281/zenodo.1466135 The initial testing dataset, which comprises three 3D mesh models of real humans bones (a humerus, a femur and a tibia, which are part of the Athens modern reference skeletal collection), is also freely available at https://doi.org/10.5281/zenodo.1466962 and may be used with the CSG Toolkit for demonstrating its operation.
An additional dataset comprising eight bilateral bones (humerus, ulna, femur, and tibia) is also available at https://doi.org/10.5281/zenodo.6614647 for testing and demostration purposes.