I’m having a couple issues with the SaveImages module that I’m pretty sure there must be an easy fix to. If I input my 2 channel image (green & red) as a gray flexfile, and then use the GraytoColor module, I can see in the module window that if I tell CP which channel is green, which is red, and to leave the blue channel black (I’ve chosen RBG), it can correctly color the images. However, when I add in 3 SaveImages modules to save the green, the red, and the overlay, this module also asks me to choose a color map. However, there’s no color map that matches the color scheme I’d like to save, which is the black>green spectrum, and the black>red spectrum that I see in the GreytoColor module window. In fact, the vast majority of the color maps lead to all black tiff files being saved.
I’m also having a problem obtaining the naming nomenclature I’d like. In each loaded flexfile, there are 4 sites imaged, and I’d like to save each colored image as either:
originalfilename_gfp_1 (or 2,3,4)
originalfilename_rfp_1 (or 2,3,4)
originalfilename_overlay_1 (or 2,3,4)
But I can’t seem to get this pattern with any combination of options. It seems like I can either get the prefix (gfp,rfp or overlay) using the “save using original file name” option, OR the field number (1,2,3,4) using the save using sequential numbers option, but not all. As a result, when I process multiple images, it always overwrites something.
Help would be much appreciated,