Batch process peak detection using Lag, Threshold, Influence

This program was organized by Aaron Miller from online references to using Lag Threshold and Influence to detect peaks in signals.  The signal here is the excel output from a plot of a surfactant protein D dodecamer (plot of a single hexamer, CRD to CRD shown here) which was subjected to L-5, T-1, I-0.01. The peaks are identified (black line series) while the actual plot is shown as the blue line. Using this csv export I added the peak widths and heights using CorelDRAW. I will convert height into grayscale, and width into nm.  Itdid take several minutes to create the bar graph which has been colored in accordance with known, as well as yet unidentified peaks which I have consistently observed over many plots of nearly a hundred dodecamers of surfactant protein D.


1) pie in the sky purpose = adding this peak finding option to ImageJ (which someone else will have to do (LOL)).

2) select just a few of the image processing programs, filters and masks that are free, optimal, easy, and produce images that can be analyzed,  and likewise, find signal processing programs that are free, easy  to use and identify which settings produce the most useful data for statistical analysis of images obtained from microscopy.

CRD=carbohydrate recognition domain (orange); Neck domain (yellow); unknown, wide peak (white); unknown low and narrow peak (pink); unknown large relatively tall peak adjacent to the glycosylation peak(s) (dark green); glycosylation peak(s) (light green); unknown tiny peak between N termini peak and glycosylation peaks (purple); N termini peak(s) (peach). Actually the halves of the hexamers should be identical however, the artifacts that arise from processing (true of all microscopy) show that not all elements are present in all tracings.  Eg, the neck domain is sometimes covered up by the CRD domain as the former is largely nested under each of the three globby CRD in each trimer. How I trace the segmented, 1px line over the image is hugely important, and aim for the brightest places along the length of the hexamer. (Image used for this plot has been shown on this site so many times that posting it again just wastes space (LOL)).


plot of grayscale peaks found along a hexamer of surfactant protein D

COMMING SOON: Are there instances where people can more accurately identify peaks than image and signal processing algorithms?