Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks

Johannes Stegmaier, Jens C. Otte, Andrei Kobitski, Andreas Bartschat, Ariel Garcia, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Konradin Metze
2014 PLoS ONE  
Automated analysis of multi-dimensional microscopy images has become an integral part of modern research in life science. Most available algorithms that provide sufficient segmentation quality, however, are infeasible for a large amount of data due to their high complexity. In this contribution we present a fast parallelized segmentation method that is especially suited for the extraction of stained nuclei from microscopy images, e.g., of developing zebrafish embryos. The idea is to transform
more » ... e input image based on gradient and normal directions in the proximity of detected seed points such that it can be handled by straightforward global thresholding like Otsu's method. We evaluate the quality of the obtained segmentation results on a set of real and simulated benchmark images in 2D and 3D and show the algorithm's superior performance compared to other state-of-the-art algorithms. We achieve an up to ten-fold decrease in processing times, allowing us to process large data sets while still providing reasonable segmentation results. Citation: Stegmaier J, Otte JC, Kobitski A, Bartschat A, Garcia A, et al. (2014) Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks. PLoS ONE 9(2): e90036.
doi:10.1371/journal.pone.0090036 pmid:24587204 pmcid:PMC3937404 fatcat:5hunpa7k6vc5jgbjthn2x5pesm