TAD locations are defined by applying an algorithm to Hi-C data. For example, TADs are often called according to the so-called "directionality index". The directionality index is calculated for individual 40kb bins, by collecting the reads that fall in the bin, and observing whether their paired reads map upstream or downstream of the bin (read pairs are required to span no more than 2Mb). A positive value indicates that more read pairs lie downstream than upstream, and a negative value indicates the reverse. Mathematically, the directionality index is a signed chi-square statistic.
The development of specialized genome browsers and visualization tools such as Juicebox, HiGlass/HiPiler, The 3D Genome Browser, 3DIV, 3D-GNOME, and TADKB have enabled us to visualize the TAD organization of regions of interest in different cell types.