Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

Abstract

Abstract. X-ray microtomography can visualize 3D structures of biological soft tissues at cellular to subcellular resolution. Such 3D structures are composed of a great number of cells and extracellular matrices that should be assigned separately as tissue constituents. Here, we report a method for building a skeletonized model of the human brain network in a 3D distribution map of linear absorption coefficients determined by microtomography. The 3D models of neurons were automatically built by using a Sobel filter and manually edited via a graphical interface. The simplification of the 3D coefficient map facilitates understanding of microtomographic structures composed of huge numbers of voxels. We suggest that x-ray microtomography along with model building in the 3D coefficient map is a potential method for understanding 3D microstructures relevant to biological functions, like x-ray crystallography in molecular biology.

Three-dimensional network of Drosophila brain hemisphere

“…The obtained radiographs were subjected to convolution-back-projection calculation using the program RecView (Mizutani et al, 2011; available from http://www.el.u-tokai.ac.jp/ryuta/) accelerated with CUDA parallel-computing processors. In total, 700 tomographic slices perpendicular to the sample rotation axis were reconstructed from one dataset with this calculation, giving linear absorption coefficients at 8 keV in a cylindrical region with a diameter of 2000 voxels and height of 700 voxels.…”

“…A three-dimensional region of 840  1250  1200 voxels of the obtained image covering the left half of the brain was subjected to the model building procedure by using the program MCTrace (Mizutani et al, 2011; available from http://www.el.u-tokai.ac.jp/ryuta/). Neuronal processes were traced by tracking the absorption coefficient distribution down to 19.4 cm -1 .…”

“…Node coordinates of a congested neuropil were placed and connected while the three-dimensional map of absorption coefficients was viewed. Sparsely distributed structures were built by automatic tracing (Mizutani et al, 2011) and examined manually afterward. To accelerate these building procedures, functions specially designed for model manipulation, such as edit functions that require minimum manual interventions and comment functions for attaching comments to model nodes, were implemented.…”

Application of three‐dimensional computed tomography in craniofacial clinical practice and research

“…Intra‐operative imaging capabilities of the pulp chamber to guide endodontic treatment would represent a quantum leap in its application in dental practice. Collaborations between various science disciplines in X‐ray optics and structural biology have helped in novel imaging of structures, such as human brain circuits, but much work needs to be done to unravel the mysteries behind 3D cellular and subcellular structures and their biological functions . Ongoing technological developments hold promise for further progress in cellular and molecular biology as part of craniofacial phenomics research, with direct implications in improving diagnosis and treatment planning.…”

The case for emulating insect brains using anatomical “wiring diagrams” equipped with biophysical models of neuronal activity

“…For imaging soft tissue, XRM requires a high-Z contrast agent. Although XRM has lower resolution than EM, it can be performed much more efficiently for larger tissue volumes while still retaining a resolution sufficient to observe dendritic and axonal processes (Mizutani et al, 2011). In addition, XRM is a nondestructive method.…”