Our facility users have been reporting an odd display issue with some MicroManager (V1.4) multichannel files when opening them in FIJI. For some reason for one of the channels, FIJI thinks it should be showing it in an 8-bit range so the second channel looks totally saturated. Once you click reset on the B&C window, it fixes and goes out to the min and max values of the image as expected. I’ve attached an example file so anyone else can try it out.
It does seem to only ever happen to the final channel in a multi channel stack (we’ve seen it in both 2 and 3 channel stacks) and it is inconsistent behaviour (for example, a user will see this on 15 out of 17 images on a day or something). We have seen it on one of our MicroManager run microscopes for a while but now started seeing it on a second one and we really don’t know why. It is only a display issue of course, but users do find it quite concerning when they open an image and they think it’s fully saturated and have to open brightness and contrast to reset every time so I would be interested in working out why it happens.
I’ve attached an example image and have seen this behaviour through several version of FIJI (though currently on 1.53c).
Note: If I force it to open through Bio-Formats instead of drag and drop, I don’t see this problem but then the LUTs are incorrect (as I’ve talked about before in this post, Bio-Formats import of μManager tiffs have incorrect LUTs).