Analyzing swath profiles

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Analyzing swath profiles

Peter Sak
        I am new to ImageJ and am looking for a way to analyze stained photomicrographs.  I suspect that what I am hoping to accomplish has already been done by others and would greatly appreciate any suggestions or scripts.  As background, I am working with samples that have been stained using a blue-colored epoxy that does not occur naturally in the slides.  I would ideally like to accomplish the following two goals.  (1) Threshold the image in a way that I can isolate and map the spatial distribution of blue (epoxy filled) pixels across the field of view and create a binary map representing the presence or absence of the thresholded pixels.  Then I would   Create a table of points that can be used to plot profiles or line scans.  The line scans will report the concentration (%) of blue pixels within a user-defined rectangular area where each point represents an integrated value across the column of pixels oriented perpendicular to the line traverse.  This second objective appears to be closely related to the RGB Profiler tool.  Any suggestions or scripts would be greatly appreciated.

Many thanks in advance,

Peter Sak
Associate Professor
Department of Earth Sciences
Dickinson College
Carlisle, PA 17013

Telephone: (717) 245-1423
Fax: (717)-245-1971

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