Automating dicentric chromosome detection from cytogenetic biodosimetry data
We present a prototype software system with sufficient capacity and speed to estimate radiation exposures in a mass casualty event by counting dicentric chromosomes (DCs) in metaphase cells from many individuals. Top-ranked metaphase cell images are segmented by classifying and defining chromosomes with an active contour gradient vector field (GVF) and by determining centromere locations along the centreline. The centreline is extracted by discrete curve evolution (DCE) skeleton branch pruning and curve interpolation. Centromere detection minimises the global width and DAPI-staining intensity profiles along the centreline. A second centromere is identified by reapplying this procedure after masking the first. Dicentrics can be identified from features that capture width and intensity profile characteristics as well as local shape features of the object contour at candidate pixel locations. The correct location of the centromere is also refined in chromosomes with sister chromatid separation. The overall algorithm has both high sensitivity (85 %) and specificity (94 %). Results are independent of the shape and structure of chromosomes in different cells, or the laboratory preparation protocol followed. The prototype software was recoded in C++/OpenCV; image processing was accelerated by data and task parallelisation with Message Passaging Interface and Intel Threading Building Blocks and an asynchronous non-blocking I/O strategy. Relative to a serial process, metaphase ranking, GVF and DCE are, respectively, 100 and 300-fold faster on an 8-core desktop and 64-core cluster computers. The software was then ported to a 1024-core supercomputer, which processed 200 metaphase images each from 1025 specimens in 1.4 h.
|Journal||Radiation Protection Dosimetry|
Rogan, P.K. (Peter K.), Li, Y. (Yanxin), Wickramasinghe, A. (Asanka), Subasinghe, A. (Akila), Caminsky, N. (Natasha), Khan, W. (Wahab), … Knoll, J.H. (Joan H.). (2014). Automating dicentric chromosome detection from cytogenetic biodosimetry data. Radiation Protection Dosimetry, 159(1-4), 95–104. doi:10.1093/rpd/ncu133