TINA is a tool we developed for the analysis of 3D images of network structures. The original application was to study confocal microscopy images of osteocyte networks, i.e., cells which are embedded within the mineralized bone matrix and are connected to each other by dendritic cell processes. The software package as well as its application to bone structures will be presented.
TINA is a tool we developed for the analysis of 3D images of network structures in biological materials. The original application was to study confocal microscopy images of osteocyte networks, i.e., cells which are embedded within the mineralized bone matrix and are connected to each other by dendritic cell processes. The analysis of the network topology starts with loading of the images, thresholding and segmentation. The binary images are then skeletonized, and converted into a NetworkX graph. The NetworkX library does not only provide many standard graph algorithms but also provides a data structure for further customized evaluations. The focus of the tool is to quantify the density of the network as well as orientation of both, the cells as well as the connection of cells. TINA also comes with a customized visualization of the network structures based on mayavi. The SciPy ecosystem provides a suitable environment for developing such an analysis framework, which can be easily applied to many samples to account for the high structural variability of biological samples. Analyzing the osteocyte network in healthy human bone we found that the network structure allows conclusions of how bone is formed. The alignment of the network correlates with the fibrous component of bone material, collagen, which was imaged by second harmonic generation microscopy. Publishing TINA under the BSD license allows the direct application of the tool on comparable images to compare osteocyte networks in different bone samples (species, age, diseases) but also to customize it to individual research questions. So far, TINA has also been used to analyze micro CT scans of the Haversian system i.e., a network of blood vessels also located in the bone, the foam-like trabecular bone, as well as tubuli in elephant tusk.  A. A. Hagberg, D. A. Schult, and P. J. Swart. Exploring network structure, dynamics, and function using NetworkX. In Varoquaux, G., T. Vaught, and J. Millman, editors, Proceedings of the 7th Python in Science Conference, 11 – 15, Pasadena, CA USA, 2008.  P. Ramachandran and G. Varoquaux. Mayavi: 3d visualization of scientific data. Computing in Science & Engineering, 13(2):40–51, March 2011. doi: 10.1109/MCSE.2011.35.