For ImageJ version 1.52i and newer the ROI selection of the source image does not work together with OBP any more. The size of the ROI influences the analysis region but the image itself is not cropped correctly.
Change in the ij API found: the ImagePlus.duplicate() method which is used for obtaining the image does not crop to ROI by default anymore.
Solution: use the .crop() method instead. To be released with 1.4.2.
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Change in the ij API found: the ImagePlus.duplicate() method which is used for obtaining the image does not crop to ROI by default anymore.
Solution: use the .crop() method instead. To be released with 1.4.2.