The Xmipp is a software package for cryo-EM data reconstruction developed by CNB CSIC. GPU-accelerated versions of the hotspots in Xmipp are developed as a joint effort of ICS MUNI and CNB CSIC.

The novel version of an algorithm allowing Xmipp to analyze the continuous heterogeneity of a specimen (typically a macromolecule) was developed by CNB. In its current implementation, multi-core CPUs are utilized. The processing speed of the current implementation is better than the older algorithm but still limits its practical usage.

The master thesis will focus on GPU acceleration of the new algorithm for continuous heterogeneity analysis. The bottleneck of the algorithm is the forward and backward interpolation of the voxel space. The student will work on the forward interpolation, implement and optimize the CUDA kernel, which replaces the bottleneck's implementation and integrates this kernel into Xmipp. Furthermore, the student analyzes the rest of the CPU code and introduces additional optimizations if necessary. The thesis will evaluate the original CPU-based implementation, the new GPU-based implementation, and proposed optimizations of the GPU-based implementation.