11 Dec 2023

Trabecular Segmentation Workflow for Murine Tibial Bone

Here we provide a workflow to easily obtain the segmentation of trabecular bones.


The segmentation of the trabecular bones can be challenging. This Xtra provides a workflow that combines the watershed and thresholding tools with a recipe to easily obtain the separation of the trabecular bones from the epiphysis region in murine tibial bone. 

The workflow provides a method for generating markers as well as a recipe to segment the trabeculae. 

Please refer to the corresponding author for more information about the usage. 

Additional resources: the Xtra How to perform trabecular and cortical bone segmentation introduces another strategy to segment trabecular bones. 

This content is a derivative work done by Dr. Eva Herbst, published under CC-BY-SA (a CC-BY Share-alike license)  Creative Commons license. You may use this derivative work under the same license. The datasets distributed within this Xtra are courtesy of the authors of the publication, for the educational purpose presented here. Publications based on the ideas presented in this Xtra must cite the below-mentioned reference. 

Data courtesy of Dr. Eva Herbst.  Eva C. Herbst et al., 2021 - Royal Society Open Science. Please cite also the code (doi.org/10.5281/zenodo.4761679) for the method. If using the scans, please cite both the paper and the Figshare dataset (https://doi.org/10.6084/m9.figshare.14098052.v4).