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I am having some issues with the Cairn Image Splitter plugin for ImageJ, after using a dual excitation / dual emission dye.
Image acquistion was done with OptoFluor (CAIRN's version of MetaFluor), using 340/380 excitation, and 450/520 emission. MetaMorph's image splitting software doesn't recognise some of the images properly, whereas they show up and open properly in ImageJ (used on a Mac, ran with the Leopard OS). But I seem to struggle using the above mentioned plugin to separate the images.
I have managed to save an alignment that was perfectly aligned, but when I try to use this saved alignment on another image it just creates two images of the same channel.
Also, I am having trouble getting batch processing to work, although this may have something to do with the fact that my saved alignment doesn't seem to work properly. When I select the source file/directory, it does not seem to process all the images, but comes back with an error message that it did not find any images.
Does anybody haveany advice on where I may be going wrong? Any suggestions to help analysing the data are highly appreciated!!!
Thanks a lot,
Katja
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