danuserlab / u-probe Goto Github PK

Requested by Hahn lab to explore possibilities for performing a pre-registration step.

I personally have had good luck with this: https://bigwww.epfl.ch/thevenaz/stackreg/

Does appear to be a wrapper: https://www.mathworks.com/matlabcentral/fileexchange/45633-stackregwrapper

Please in the readme file provide the commands to launch the GUI

Hi,

I got an error message when I tried to process a set of ratiometric imaging. Here is the detailed error message.

MATLAB Version 24.1.0.2537033 (R2024a)

Operating System: Microsoft Windows 11 Home Version 10.0 (Build 22631)
Java VM Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

-- Step 10: Ratioing

Undefined function 'nanmax' for input arguments of type 'double'.

Error in ratioMovie (line 359)
ratMax = max(ratMax,nanmax(currRatio(:)));

Error in Process/run (line 255)
obj.funName_(obj.getOwner(), varargin{:});

Error in packageGUI_RunFcn>userfcn_runProc_dfs (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)));

The prepare button that used to let you organize your data into the appropriate folder structure is not functioning anymore in this version. Nothing happens after it gets pressed.
Tested with MATLAB versions 2017 and 2020.

Hi,

I recently encountered a problem using the BiosensorpackageGUI. When I tried to read a file (i.e. a dark current correction folder) in my local disk, MatLab confused the backslash "" in the direction with the function "Escape".

I got the setting error "Dark current correction image-D:"

And MatLab gives this warning:

Warning: Escaped character '\D' is not valid. See 'doc sprintf' for supported special characters.

In DarkCurrentCorrectionProcess/sanityCheck (line 89)
In darkCurrentCorrectionProcessGUI>pushbutton_done_Callback (line 166)
In gui_mainfcn (line 95)
In darkCurrentCorrectionProcessGUI (line 61)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)darkCurrentCorrectionProcessGUI('pushbutton_done_Callback',hObject,eventdata,guidata(hObject))

Do you have any idea how to fix this problem? I tried it on MatLab 2024b and MatLab 2020b. The problem occurs for both versions.

Thank you!

Hello,

I am having issues with the cropping step if my data set has more than two channels. The following message comes up when I try (see attached picture).

When using MSA segmentation it is using the raw data instead of cropped images (see attached first and second image). This doesn't happen to be the case when I use Otsu thresholding (third image).