I have a 4 channel (DAPI, eGFP, Cy3, Cy5) z-stack image I took on a Leica Confocal, resulting in an LIF project file that is fairly large. I can put it into the LAS X application and see/export it as a TIFF and then put that file into ImageJ.
My usual process (done on OIF files) is doing the max-projection z-stack followed by separating the channels. However, for some reason when I do this the end output is only 3 channels. They’re called “red”, “blue”, and “green”, but they don’t perfectly overlay with the 4 channels, so I am confused.
Also, when I do this with OIFs, it splits into channels it labels C1-, C2-, C3-, and C4-, which is different from the labels I get from doing the same steps with the LIF.
Does anyone know what is going on or a way to work around this? I just want to split the channels into four greyscale pictures for later image analysis and don’t want to lose any image quality.
Thank you for any and all help!