Liisa Hirvonen edited Method.tex  over 8 years ago

Commit id: abc18e1771ea44aecc2dd879e0448b6d55a6f9a3

deletions | additions      

       

  %\subsection{Data processing}  The frames containing single photon events were processed with the ThunderSTORM \cite{Ovesny2014} superresolution imaging plug-in for ImageJ.Due to memory limitations, the USAF data was processed in 6$\times$5,000 and the cell data in 3$\times$2,000 image stacks.  The frames containing single photon events were processed with the ThunderSTORM \cite{Ovesny2014} superresolution imaging plug-in for ImageJ. Due to memory limitations, the USAF data was processed in 6$\times$5,000 and the cell data in 3$\times$2,000 image stacks. The software first detects the events from the noise background, and an approximate localisation algorithm locates the center pixel of each event. A sub-pixel localisation algorithm then calculates the center of the events with greater resolution. The software camera parameters were set to 80.0~nm pixel size and 36 photoelectrons per A/D count. The base level varied between image stacks due to fluctuations in the EBCCD temperature, and was set to the average minimum grey value for the image stack in the range of 100-140 A/D counts. A wavelet (b-spline) image filter was applied with order of 3 and scale of 2.0. For the approximate localisation of the events, the centroid of connected components method was used with a peak intensity threshold (PIT) of 2*std(Wave.F1) for the USAF data, and a PIT of 1.5*std(Wave.F1) for cell data, with the watershed algorithm enabled for all data.