Detecting differences at the cellular level is an ongoing problem which, if successfully addressed, could help solve several prevalent ailments, including cancers and prenatal diseases. Normal tissue function requires appropriate cell positioning and directional motion. This property, known as chirality, can be altered by genetic and environmental factors, leading to, for example, birth defects and tumor formation. Current methods to diagnose cancer are based on biomarkers, imaging, and analysis of tissue specimens. In most cases, the findings from one assay (such as imaging) are corroborated by other assays (such as pathological evaluation of biopsy samples). 2D cultures do not fully represent the dynamics of tissue polarization and cell-cell interactions during tissue formation in vivo. Moreover, it is not possible to measure chirality of certain cells with 2D cultures. In this technology, a method was developed for determining the chirality of a cell. The cell is cultured in a three-dimensional substrate including base and top layers of cell growth material. The direction of the from a nucleus of the cell to an organelle of the cell along a plurality of orthogonal sections of the three dimensional substrate is then measured to determine its chirality. Applications of this technology include toxicity screening for potential teratogens causing birth defects, birth defect screening with the cells from placenta or through amniocentesis, quality control of cell function, diagnosis of other diseases such as cancer, etc.