Discover biological features using composite images

A computer-implementable image processing pipeline, comprising:

• a collector for collecting data from a process in which prepared biological samples are obtained from expression experiments under different treatment conditions;
• an image processor for processing the data from the collector and forming a composite image;
• and
• an image feature extractor for extracting feature characteristics from the composite image, which include peaks, isotope groups, and charge groups, wherein the image feature extractor is configured to identify isotope peaks from connected non-zero pixels on a composite image;
• and split identified isotope peaks that are composed of two or more isotope peaks in a mass/charge direction, a retention time direction, or both.

A computer-implementable image processing pipeline, comprising:

• a collector for collecting data from a process in which prepared biological samples are obtained from expression experiments of different treatment conditions;
• an image processor for processing the data from the collector and forming a composite image;
• and
• an image feature extractor for extracting feature characteristics from the composite image, which include peaks, isotope groups, and charge groups, wherein the image feature extractor is configured to compute isotope group characteristics that are selected from a group consisting of charge state, mono-isotopic mass/charge, and peptide mass, and further wherein the image feature extractor is configured to identify an isotope group with only one isotope peak as belonging to a charge group with an unknown charge.

A computer-implementable image processing pipeline, comprising:

• a collector for collecting data from a process in which prepared biological samples are obtained from expression experiments of different treatment conditions;
• an image processor for processing the data from the collector and forming a composite image;
• and
• an image feature extractor for extracting feature characteristics from the composite image, which include peaks, isotope groups, and charge groups, wherein the image feature extractor is configured to remove streaks in a retention time direction by:
• setting pixels, whose intensities rank in the lower ninety percentile, of a rasterized LC/MS image to zero to create a threshold LC/MS image;
• creating an original bit mask;
• performing a morphological open operation in the retention time direction on the original bit mask using a maximum peak width to reveal retention time streaks;
• executing a conditional dilation operation to dilate the retention time streaks back to their original sizes in the retention time direction and in the mass/charge direction;
• inverting the original bit mask to form an inverted bit mask;
• and
• multiplying the inverted bit mask with the rasterized LC/MS image to remove the retention time streaks.