Preset channel colors in configuration file


I am looking for a way to preset the color of each channel directly in the hardware configuration file. More specifically if for example my configuration file contains a group called ‘Channel’ with presets ‘DAPI’, ‘FITC’, etc, I would like to associate the appropriate color (blue, green, etc respectively) with each preset. This would result in the color mode in the image inspector changing depending on what channel is selected when snapping an image, going live and ideally when adding channels in MDA.

I’m assuming this is possible?


This more or less works as you describe, except that colors are stored within the user profile in the UI, rather than in the hardware configuration file (reason: colors are not hardware;). There have been recent fixes to this mechanism, so please try the latest nightly build. You need to select the colors once (for instance in the MDA dialog), and you should be good to go.

Thanks Nico, this works just as you say. Is that something that can be modified out of Micromanager in the profile.txt file or is the information stored in a different file?

There is no support for editing the profiles directly. However, you can duplicate them (in the UI), or you can copy (and edit) the files if you so desire. On Windows they are stored in currentUserName\AppData\Local\ Micro-Manager. Probably in JSON format, but I am not sure.