So this is something I’ve noticed for a while (through a couple of Bio-Formats versions at least) but have never really bothered to report till now cause of laziness I guess.
So if, in FIJI, I drag and drop (or use File>Open) a μManager (version 1.4) multi-channel ome.tiff the LUTs match those used at acquisition (in the sample 4 channel file that is green, red, cyan, blue), however, if I select the file through the Bio-Formats importer then the LUTs are totally different and in fact two are the same which is espeically not useful (magenta, yellow, magenta, red). This happens with either “Composite” or “Colorized” setting in the Bio-Formats window. If I use “Default” then the image just opens as all greyscale.
Sample file here 18_11_MMStack_Pos0.ome.tif (11.1 MB)
Edit: the same LUTs (magenta, yellow, magenta, red) are applied to the channels when the file is opened in QuPath too.