Anakoi
commented
6 days ago I also receive a warning in the end in the command window as well. I paste all the displayed messages below:
Saving results... Finished Correcting! Using previously specified correction image directories... The folder E:\Pengning\20241115 ChemoG Talin test\test\Results\BiosensorsPackage\shade_corrected_images\shade_corrected_images_for_channel_1 already existed. Cleaning the folder ... The folder E:\Pengning\20241115 ChemoG Talin test\test\Results\BiosensorsPackage\shade_corrected_images\shade_corrected_images_for_channel_2 already existed. Cleaning the folder ... Starting shade correction... Loading and processing correction image(s)... Applying shade correction to images... Shade correcting channel 1... Correcting images from "E:\Pengning\20241115 ChemoG Talin test\test\Results\BiosensorsPackage\dark_current_corrected_images\dark_current_corrected_images_for_channel_1", resulting images will be stored in "E:\Pengning\20241115 ChemoG Talin test\test\Results\BiosensorsPackage\shade_corrected_images\shade_corrected_images_for_channel_1" Using correction images from E:\Pengning\20241115 ChemoG Talin test\FakeShades Shade correcting channel 2... Correcting images from "E:\Pengning\20241115 ChemoG Talin test\test\Results\BiosensorsPackage\dark_current_corrected_images\dark_current_corrected_images_for_channel_2", resulting images will be stored in "E:\Pengning\20241115 ChemoG Talin test\test\Results\BiosensorsPackage\shade_corrected_images\shade_corrected_images_for_channel_2" Using correction images from E:\Pengning\20241115 ChemoG Talin test\FakeShades Saving results... Finished Correcting! Finished importing external data! Warning: Cannot create background masks because some channels do not have foreground masks! Please segment these channels before creating background masks!
I tried to use the external mask generated by ImageJ in the Segmentation step by choosing the External Segmentation option. Every thing before Step 4 runs normally. However, in Background Mask step it gives me error (shown at the end of this communication). The strange thing was that the program let me pass the step 4 once, for completely unknown reasons. Other times I just keep getting the same failures. I attach a test sample here: TestSample.zip
MATLAB Version 9.14.0.2286388 (R2023a) Update 3
MATLAB License Number: 334062
Operating System: Microsoft Windows 10 Enterprise Version 10.0 (Build 19044)
Java VM Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Movie 1 - E:\Pengning\20241115 ChemoG Talin test\test\Results\movieData.mat:
-- Step 5: Background Mask
Intermediate brace '{}' indexing produced a comma-separated list with 0 values, but it must produce a single value when followed by subsequent indexing
operations.
Error in createMovieBackgroundMasks (line 191)
movieData.processes{iP}.outFilePaths(p.ChannelIndex(j)));
Error in Process/run (line 255)
obj.funName_(obj.getOwner(), varargin{:});
Error in packageGUI_RunFcn>userfcn_runProcdfs (line 635)
userData.crtPackage.processes{procID}.run(); % throws exception
Error in packageGUI_RunFcn>start_processing_movies_in_series (line 221)
userfcn_runProc_dfs(procID, procRun{iMovie}, handles); % user data is retrieved, updated and submitted
Error in packageGUI_RunFcn (line 166)
movieException = start_processing_movies_in_series(movieRun,handles,movieException,procRun);
Error in packageGUI_OpeningFcn>@(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)) (line 432)
set(handles.pushbutton_run, 'Callback', @(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)));
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