Aliakbar Jafarpour

Aliakbar Jafarpour, Holger Lorenz

Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different images in different groups; 3) different interactive visualization schemes; and 4) interactive realistic simulation of different cellular processes for validation and optimal problem-specific adjustment of image acquisition parameters (tradeoff between speed, resolution, and quality with feedback from the very final results). The collection of programs is primarily developed for the common bio-image analysis software ImageJ (as a single Java Plugin). Some programs are also available in other languages (C++ and Javascript) and may be run simply with a web-browser; even on a low-end Tablet or Smartphone. The programs are available at https://github.com/nurlicht/CellulyzerDemo

Aliakbar Jafarpour

Single particle 3D imaging with ultrashort X-ray laser pulses is based on collecting and combining the information content of 2D scattering patterns of an object at different orientations. Typical sample-delivery schemes leave little or no room for controlling the orientations. As such, the orientation associated with a given snapshot should be estimated after the experiment. Here we present an open-source code for the most rigorous technique having been reported in this context. Some practical issues along with proposed solutions are also discussed.