danuserlab/u-shape3d

Detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.

u-shape3d's Issues

array exceeds maximum array size preference

I am trying to run the example provided in the User guide. When running step 3, Matlab throws the following error:
Error using smoothpatch (line 102)
Requested 1928440402996x1 (14368.0GB) array exceeds maximum array size preference (31.9GB).

I tried disabling the array size limit in Matlab, but the error is still there.
I am also very surprised at the array size (14TB ??).

Any help would be greatly appreciated. I paste below the Detailled error report.
Best,
Nicolas

`MATLAB Version 9.10.0.1602886 (R2021a)
MATLAB License Number: 113029
Operating System: Microsoft Windows 10 Professionnel Version 10.0 (Build 19041)
Java VM Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Movie 1 - E:\Documents\MATLAB\ushaped3D_Output\movieData.mat:

-- Step 3: Mesh

Error using smoothpatch (line 102)
Requested 1928440402996x1 (14368.0GB) array exceeds maximum array size preference (31.9GB). This might cause MATLAB to become unresponsive.

Error in meshMovieMD (line 167)
parfor t = 1:MD.nFrames_ % can be made a parfor loop

Error in Process/run (line 254)
obj.funName_(obj.getOwner(), varargin{:});

Error in packageGUI_RunFcn>userfcn_runProc_dfs (line 629)
userData.crtPackage.processes_{procID}.run(); % throws exception

Error in packageGUI_RunFcn>start_processing_movies_in_series (line 215)
userfcn_runProc_dfs(procID, procRun{iMovie}, handles); % user data is retrieved, updated and submitted

Error in packageGUI_RunFcn (line 160)
movieException = start_processing_movies_in_series(movieRun,handles,movieException,procRun);

Error in packageGUI_OpeningFcn>@(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)) (line 382)
set(handles.pushbutton_run, 'Callback', @(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)));
Please verify your settings are correct. Feel free to contact us if you have question regarding this error.

Please help us improve the software by clearly reporting the scenario when this error occurs, and the above error information to us (error information is also displayed in Matlab command line).

For contact information please refer to the following URL:
http://www.utsouthwestern.edu/labs/danuser/software/ `

The image brightness is saturated after doing deconvolution

I want to use data that I have acquired using SPIM. But when I choose deconvolution and mesh, after deconvolution I get that image brightness is saturated and then in the next step (mesh) software freezes. I don´t know what could be the problem. Is there maybe a way to adjust psf file to fit to our set-up? Or is there some other way to deal with this problem? Thank you in advance

Problem at Step 5

Hi, I used the example data as input. However, when the step is 5, the system shows the error message as follow. Could you help me identify what the problem is? Thank you.

--Step 5: SurfaceSegmentation

Caused by:
Error using calculateMutualVisibilityPair (line 71)
Undefined function 'nanmean' for input arguments of type 'double'.

Error on Windows (Win10) Unable to read file ... Input cannot be a directory

While running runDendSegment.m, we encountered the following error on Windows.

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

In patchDescriptionForMergeMeshMD (line 104)
In Process/run (line 249)
In startProcess (line 105)
In morphology3D (line 143)
In runDendSegment (line 79)
Error using load
Unable to read file 'D:\Siamak_stuff\u-shape3D-master'. Input cannot be a directory.

Error in patchDescriptionForMergeMeshMD (line 104)
sStruct = load(sprintf(surfacePath, c, t)) %Siamak Lamellopeia is chocking here

Error in Process/run (line 249)
obj.funName_(obj, varargin{:});

Error in startProcess (line 105)
process.run(parameters);

Error in morphology3D (line 143)
startProcess(MD, 'Morphology3DPackage', 'PatchDescriptionForMerge3DProcess', p.patchDescribeForMerge, p.control.patchDescribeForMergeReset)

Error in runDendSegment (line 79)
morphology3D(MD, p)

Error with MD variable for runKrasTrain (Example 4 in User Guide)

Hi! I am trying to go through Example 4 in the User Guide to learn how to train my own SVM. I've been consistently running into the same error when running runKrasTrain.m:

Cell 1: Cell1
The provided path is not the path to a Matlab variable
Unrecognized function or variable 'MD'.

Error in clickOnProtrusions (line 96)
sanityCheck(MD);

Error in runKrasTrain (line 60)
clickOnProtrusions(p)

For some reason, clickOnProtrusions is not recognizing the MD variable in my workspace - it keeps getting stuck on lines 90-96 of clickonProtrusions.m when it tries to load the MovieData object and then run sanityCheck(MD). When I type in MD in the command line, Matlab registers that MD exists. I've checked the directory path in the MD variable and made sure it matches what I inputted for the analysisDirectory variable in line 38 of runKrasTrain.m.

I'm quite stumped on how to troubleshoot and would appreciate any insight! Thank you so much!

Error running 1 of 2 channels for Step 3

Hi! I am trying to generate the surface mesh for one channel of my image stack. I have loaded both channel stacks as separate channels in a movie. When I start at Step 3 and only select 1 of the 2 channels, I get the following error report:

--Step 3: Mesh                                                                                                                                                                                   
                                                                                                                                                                                                 
Caused by:                                                                                                                                                                                       
Intermediate brace '{}' indexing produced a comma-separated list with 0 values, but it must produce a single value when followed by subsequent indexing operations.   

I do not have this issue when I run Step 3 with a movie containing only 1 channel. I am making sure to check "use deconvolved", so that does not seem to be the issue. Is there a step to handling multi-channel movies that I might be missing that would generate this indexing error? Thanks!