The contrast transfer function (CTF) of the selected particles from each film was determined with EMAN2 and images that showed visible Thon rings in the power spectrum to high resolution and no indication of drift or astigmatism were selected for further processing and their CTF was corrected by phase flipping.
At the beginning of the image processing, the pair of images was corrected for relative translational shift.
The delay between the trigger signal and stimuli projection (17 ms) was corrected during data processing.
Basically, systematic errors indicate an issue in the signal processing that can be corrected by improving sensing, amplification, calibration, or by correction (Fig. 1).
During the pre-processing phase, data were corrected for PCR efficiencies (Additional file 1 and Additional file 2) and the three technical repeats were averaged.
During the pre-processing phase, data were corrected for the efficiency of the PCR (Table 1) and were averaged over the three technical repeats (considering only results that showed a standard deviation less than 0.2 within the triplicate).
Our approach avoids a subjective subselection of the set of predefined regulators, i.e. all regulators should be included in the inference in absence of prior information, and, by a post-processing step, interference is corrected.
As the first processing steps, motion artifacts are corrected and the breast region is segmented.
Before further processing, the 8 metabolite subspectra were corrected for eddy currents using water-unsuppressed spectra (n = 8), automatically corrected for frequency and phase shifts, and added together to give 128 averages.
For one metabolite spectrum eight subspectra of 16 phase cycled scans each were recorded with TR = 3 s and TE = 80 ms. Before further processing, the 8 metabolite subspectra were corrected for eddy currents using water-unsuppressed spectra (TR and TE as above), automatically corrected for frequency and phase shifts, and added together to give 128 averages.
