Having a few issues in transitioning from MM1.4 to 2

Hi all,

We’ve just started using MM2 on one of our microscopes and just noticed a couple of issues. One is that the displayed LUT colour you set in the MDA window under the colour column is incorrect for what has been set in the pick a colour menu. The image itself comes out with the correct LUTs though which is the main thing. The second thing is that after an acquisition often the shutter (Lumencor Spectra X) is left open. Autoshutter is enabled and the shutter graphic is in the closed position but the button says open so its got confused somewhere. The third thing is that if you have clicked in the exposure box of a channel in the MDA window but then you update the exposure for that channel in the main window it doesn’t sync to the MDA (sync exposure is on), perhaps that is expected behaviour? I’ve attached two problem reports that hopefully show all these issues.

Thanks for the help,


Problem Report sync exp.txt (132.1 KB) Problem Report.txt (591.9 KB)

Hi @Matt_Pearson1,

Great to see you here! Issues:

  1. I can easily reproduce this with the demo configuration. You found a bug! It would be great to report this as an issue on github (https://github.com/micro-manager/micro-manager/issues), but no worries if you do not have a github account, I’ll be happy to put it there (and this should not be hard to fix).
  2. I looked at your config file, and it has the shutter state of both the LumenCor Spectra and the ZeissTransmitted Light Shutter in there. Adding Shutter state to config files invariably leads to problems (we probably should disallow doing that, but somehow feels wrong too). If that worked correctly in 1.4, it was luck. Try taking those out of the Channel group all together and see how it goes. Also, the shutter button text indicates an action, not a state, so think “To Open” when it says “Open” (MM really thinks that the shutter is closed). Confusing, even after all these years, ideas to make this crystal clear are very welcome>
  3. There is an option (Tools > Options… " Sync exposure between MDA and main window") that probably is unchecked by default. Check it to get the behavior you like (you probably checked that in 1.4 so long ago that you forgot all about it;)

Hi Nico,

Thanks for your reply. I see you have posted the LUT issue on github already, thanks for that.

I will remove the shutter state from the channel group and see if that fixes the shutter issue. Regarding the shutter button, actually yes now you say it i’ve been confused by this before. Maybe just having a button that is the little shutter icon that you already have and remove the button that has the open/close text or have shutter written next to the icon if space allows in small text. As well as the icon animating to be open/closed could you change its colour too? One issue is that changing the colour of buttons whether they’re enabled or not is not a theme in Micro-Manager so would break from the current UI style i guess.

The sync exposure option is enabled in Options. I think it only doesn’t update if the exposure text box in the MDA window has been clicked into. I.e. if you go to update the exposure via the MDA for DAPI but then you move back to the main window, select DAPI channel and change the exposure there it won’t update that channel in the MDA because the exposure text box there is still active. Its probably a rare circumstance that this happens though.

Thanks for your support on this.


The shutter is now closing at the end of acquisition so must have been the shutter state being in the channel group as you said. Also the nightly build has fixed the issue with the active exposure text box in MDA stopping exposure sync.



1 Like