Extractor & Diaphysator: a complete ecosystem for the cartography of long bones diaphysis


(by Ján Dupej, Alizé Lacoste Jeanson, Josef Pelikán and Jaroslav Brůžek)

Extractor is a software exclusive to Windows operating system. Based on an adaptive thresholding method for boundary detection (half-maximum height as described in Spoor et al., 1993), it semi-automatically extracts periosteal and endosteal surfaces of long bone diaphysis based on three landmarks numerically positioned by the user directly on CT scans images. Extractor ensures homology of the data by using rigid registration (rotation, translation, and scaling), making it able to be further used in statistical analyses. Extractor also automatically reslices the diaphyses into virtual cross-sections along the medial axis and calculates the inner curvature.

Read our article: Dupej, J., Lacoste Jeanson, A., Pelikán, J., & Brůžek, J. (2017). Semiautomatic extraction of cortical thickness and diaphyseal curvature from CT scans. American Journal of Physical Anthropology, 164(4), 868–876. DOI: 10.1002/ajpa.23315

Download Extractor (for Windows OS only)

Download the technical documentation


(by Frédéric Santos and Alizé Lacoste Jeanson)

Diaphysator is an open-source R-Shiny application for the analysis of entire long bone diaphysis. It automatically generates maps and graphs based on cortical thickness and cross-sectional geometry, respectively. Average maps and graphs for different populations can be computed for comparative purposes. Diaphysator is able to calculate correlation coefficients and partial correlations of a given covariate (e.g. age, body mass) with the cortical thickness maps and cross-sectional geometry graphs.

Diaphysator is described in: Santos, F., Lacoste Jeanson, A. (2019). Diaphysator: An online application for the exhaustive cartography and user-friendly statistical analysis of long bone diaphyses. American Journal of Physical Anthropology, 169, 377–384. DOI: 10.1002/ajpa.23835.

Download an example of valid data set, composed of right tibiae and femora. These data file have been published in: Lacoste Jeanson, A., Santos, F., Villa, C., Banner, J., & Bruzek, J. (2018). Architecture of the femoral and tibial diaphyses in relation to body mass and composition: Research from whole-body CT. American Journal of Physical Anthropology, 167(4), 813–826. DOI: 10.1002/ajpa.23713.

How to install and use Diaphysator?

Diaphysator can be used either as an online application (available at: https://diaphysator.shinyapps.io/maps/), or as an R package hosted on GitLab. A user and installation guide is available on GitLab.

Download the technical documentation

Bug reports and suggestions

Bug reports or other requests or suggestions for Diaphysator can be made through GitLab. Furthermore, all contributions on GitLab are welcome to improve the app.


Video tutorials (recorded by Alizé Lacoste Jeanson) are available on Vimeo for both software:

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