Error when merging 2 channels


I am trying to use BiofilmQ to analyze a confocal Z-stack with 2 fluorescence channels & compare relative biomass. After successful “cubed” segmentation of both channels, I click on “Post-processing --> Merge Channels … --> 1 to 2 --> Perform task” but then I get the following error message(s) [see below]. Any idea on how to solve this?


=========== Processing image 1 of 1 ===========

  • loading cells [airystack_0.7_Airyscan Processing_pos1_ch2_frame000001_Nz19_data.mat, 94 Mb] 100% […] Done. … 3.0s
  • loading cells [airystack_0.7_Airyscan Processing_pos1_ch1_frame000001_Nz19_data.mat, 78 Mb] 100% […] Done. … 2.4s
    Undefined function or variable ‘filename_ch2’.

Error in mergeChannels (line 225)
answer = questdlg({‘Do you really want to merge the following files (non-cubed data) and following
files?’, ‘’, filename_ch1, filename_ch2, ‘’, ‘The original files are copied to “data/non-merged
data”’}, …

Error in BiofilmQ>pushbutton_tools_mergeChannels_Callback (line 3202)
mergeChannels(hObject, eventdata, handles);

Error in gui_mainfcn (line 95)

Error in BiofilmQ (line 21)
gui_mainfcn(gui_State, varargin{:});

Error in>@(hObject,eventdata)BiofilmQ(‘pushbutton_tools_mergeChannels_Callback’,hObject,eventdata,guidata(hObject))
Error using displayStatus (line 27)
Error while evaluating UIControl Callback.

Hello Elisa,

thank you so much for alerting us to this error. BiofilmQ is still in its beta version, so any feedback - especially concerning bugs - is incredibly valuable to us.

We fixed the issue and updated our BiofilmQ versions on the website, so you can now download and install a corrected version. I apologize for the inconvenience and the delay in answering to your post.

If you have any other questions or feedback, I´d be happy to hear about it :smiley:



1 Like

Thanks Hannah! This solved the problem. :+1: