Before I start, I want to thank this community for the help that it has already provided me. I have lurked for some time here but an issue in my current project motivated me to start this thread.
I am using a two photon fluorescence microscopy to make multiview reconstructions of EGFP labeled zebrafish. I have images of two channels: the emissoins from the EGFP and the one from secon harmonics generations. I can easily fuse the EGFP channel because I added fluorescent beads to the agarose gel in which the zebrafish are embedded. Unfortunately, the second harmonics channel -which does not detect the beads fluorescence- stays unmutated by the Multiview Deconvolution Plugin.
I am aware that the ImageJ page (http://imagej.net/Multi-View_Deconvolution#Multi-Channel_Multi-View_Deconvolution) outlines a method to translate the deconvolution coordinates from one channel to another channel. However, my knowledge in Java is too basic to follow this method.
Instead, I have tried fusing both channels toguether (following the method here outlined: https://microscopy.duke.edu/guides/overlay-images-imageJ) to trick Fiji into fusing them toguether. However, it seems to be able to recognize that there is more than one channel and excludes the second harmonics form the multiview deconvolution.
I was wondering if someone knew of a way to ‘fuse’ two channels in a way that tricks the Multiview Deconvolution Plugin.
Thanks in advance!