Display oddity with MicroManager files in FIJI (one channel incorrectly with 8-bit display)

IMR90_#24_14_09_20_7_MMStack_Pos0.ome.tif (16.0 MB)

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).

This happens using ImageJ, independently of Fiji. It looks like ImageJ is correctly reading the information from its its (private) TIFF tag 50839.

This fits with MicroManager using an IJMetadata tag: https://micro-manager.org/wiki/Micro-Manager_File_Formats

I’m afraid that’s as far as I got… no idea why the display settings in that tag may be unhelpfully set to 0-255 in your case.

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Hmm, I probably should have thought to load it in plain ImageJ. Thanks a lot for testing and the info.

Inconsistent behaviour is the worst because you feel like there’s going to be an answer but maybe there never will be.

Indeed, the display range for channel 2 is saved as 0-255 (open the image, Image > Show Info, look for “Display Ranges”. Micro-Manager sets these values based on how the display is set. However, the question then becomes, when does MM read these values and set them? This is easy when you save images with the floppy disk icon in the viewer, MM saves the current display settings. However, when auto-saving from the MDA, it is possible that old display settings are saved, or the settings that are active at the end of the acquisition (I am not entirely sure how that works, and different MM versions may work differently). I guess that Boiformats ignores these ImageJ-specific settings (that MM saves to make opening in ImageJ easier).

It is possible that at one point you ran an acquisition in 8-bit, and that somehow the display remembers that setting. I’ll have a look at the code to see if there is something obvious, but in general the code remembering and restoring display setting is quite tricky, and it is easy to confuse things even more.


Hi Nico

Ok I get it. So I ran the acquisition for Laura from MDA and couln’t reproduce the issue. But of course I was running acquisition in my account and I’ve never used 8 bit acquisition. Our University uses Active Directory to manage user accounts and there can be issues with Roaming profiles.

We are in the situation in Scotland where we need to do 2m social distancing from everyone except people we live with. So supporting new and less experienced users with matters like this is really challenging. We are still running MM1.4, I ought to know which version of ImageJ but I will confess I do not know. We haven’t moved to 2 because, as you may remember, we have some very old but still working (5 years later) peripheral devices and the drivers for these in 1.4 are really solid.

Would Saving golden copy of my MDA settings and getting users to load this help here?

Thanks for your thoughts.


Hi Ann,

Sharing your MDA settings will not help, as the “default” display settings are saved in the user profile. I think that in the case of Active Directory logins that mount a “home” directory, the profile will be in the user’s home directory (they are in ~/AppData/Local/Micro-Manager where AppData is usual hidden). You could potentially copy your profile to that of the user. However, if the user sets up the display correctly once, that should also be stored correctly from then on.

What are those peripheral devices? The hardware layers of 2.0 and 1.4 are exactly the same, so if a current 1.4 works, 2.0 should work as well. Transitioning your users while social distancing may be hard though. We would love your feedback, especially before the official release (later this year).

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I like that Idea, we already do that with Dragonfly. We could also delete the settings in the users home directory.

As you can see we have recently had a couple of PC deaths so my plan is to reimplement MM on the new PC using version 2.0. I’m very happy to let you know how we are getting on. Is your email still the same? Not sure if the forum is a good place for our feedback or not?

Email is still the same. Forum is fine for everything non-personal. If we solve something here, it will become searchable and may help others.

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