3D+t Terabyte Image Analysis

Completed Project



The project will develop methods for processing time series of high resolution 3D images. The goal is to obtain very high performance both with respect to result quality and computational efficiency on modern hardware.


We will demonstrate the performance of our methods using large real world inputs of developing zebrafish embryos generated by light-sheet microscopy. These datasets reach more than 10 Terabytes per embryo and will be two orders of magnitude larger than previously reported tools can handle. Large realistic, simulated inputs including ground truth will be used to quantitatively assess result quality.




Kobitski, A.; Otte, J. C.; Takamiya, M.; Schäfer, B.; Mertes, J.; Stegmaier, J.; Rastegar, S.; Rindone, F.; Hartmann, V.; Stotzka, R.; García, A.; Wezel, J. v.; Mikut, R.; Strähle, U. & Nienhaus, G. U.

An Ensemble-Averaged, Cell Density-based Digital Model of Zebrafish Embryo Development Derived from Light-Sheet Microscopy Data with Single-Cell Resolution

Scientific Reports, 2015, 5, 1-10