Home AutoQuant General Discussions

Turning channels display on/off in AQX3

 I have a 2-channel image stack  (GFP, Cy5) that is shown in Red and Green overlay. i would like to hide one of the channels to have just one channel displayed. I knew how to do it in X2 (AQX2 shows a data tree with channels separately and a checkbox for each channel) The X3 is not showing the channels separately in Data Managers in a tree display.

Is there a new trick to it?

On a related note, I how would I split a 2-channel image stack to two separate stacks in AQ3?  


Stan Vitha
Texas A&M University
Microscopy and Imaging Center   


  • Hi Stan,

    The behavior between X2 and X3 should be the same as far as the data tree. If the dataset is not showing two channels at all in the metadata Summary tab, let me know. Otherwise, the way I prefer to toggle channels is actually through the Summary tab. If you hover the mouse over a channel’s wavelength field, a checkbox will appear that allows you to toggle the channel on or off there:

    As far as splitting the set into multiple channels, there are a few ways to do it, but I think the most straightforward way is through the Save As dialog:

    1.       Select File | Save As

    2.       In the Save As dialog, look for “Export” at the upper-right. In that drop-down, select “Channels”

    3.       Press Save

    That will generate separate files for each channel, but it will also generate an XML header that will load all of the files together as a multi-channel set. You can either delete the XML header, or you can keep that around, and create new per-channel XMLs by selecting the individual channel image files in a Windows Explorer and dragging them into AQX together. That will cause AQX to treat each one separately:

  • Hi Andy,
    thank you for the tips instructions. Yes, now I can see it both ways. i did not know about the trick in the Summary tab.  and on my screen, the little triangles to unfold the data tree were so small that I missed it. All clear.
    I have another question regarding the instrument setting (objective database) - I will post as a new topic.
Sign In or Register to comment.