danuserlab / u-track Goto Github PK

Hi,
I am trying to use u-track on macOS. I installed using the instructions however once u-track through docker the GUI is not showing up. I used the following line from the instructions.
docker run -ti --rm -e DISPLAY=${ipAddress}:0.0 jennyzouutsw/utrack2018b:1.0.0 bash /execute/utrack/run_utrack.sh /opt/mcr/v95
Minor notes:
Some of the terminal based commands needs updating

1. To install xQuartz
   brew install xQuartz --cask
2. to add the IP
   had to use : ssh -Y IP #address

I can run u-track with a test dataset in 2017b or 2018b, but with MATLAB 2019b I get the following error. I'm sure it's something simple but I couldn't fix the problem, so I'm raising an issue.

MATLAB License Number: 322847                                                                                                                                                                    
Operating System: Mac OS X  Version: 10.14.6 Build: 18G1012                                                                                                                                      
Java VM Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode                                                                                         
Movie 1 - /Users/xxx/Desktop/output/movieData.mat:                                                                                                                                             
                                                                                                                                                                                                 
-- Step 1: Comet Detection                                                                                                                                                                       
                                                                                                                                                                                                 
Undefined function 'csaps' for input arguments of type 'double'.                                                                                                                                 
                                                                                                                                                                                                 
Error in optimalHistogram (line 203)                                                                                                                                                             
    cdfSpline = csaps(xData2,yData2,1./(1+mean(diff(xData2))^3/0.0006));                                                                                                                         
                                                                                                                                                                                                 
Error in cutFirstHistMode (line 165)                                                                                                                                                             
    [counts,bins,sp] = optimalHistogram(data,'smooth');                                                                                                                                          
                                                                                                                                                                                                 
Error in thresholdRosin (line 70)                                                                                                                                                                
[~,level] =  cutFirstHistMode(imageInNorm,0);                                                                                                                                                    
                                                                                                                                                                                                 
Error in detectMovieComets (line 181)                                                                                                                                                            
            thresholdRosin(thFilterDiff)*2/3;                                                                                                                                                    
                                                                                                                                                                                                 
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 424)                                                                              
set(handles.pushbutton_run, 'Callback', @(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)));  ```

Hi u-track authors/editors,

I've been using u-track to detect and track MT tip comets, as described in the Danuser Lab's paper here. I'm particularly interested in using your software to characterize microtubule instability, namely catastrophe and rescue events.

No forward or backward events have been identified, however, in the "Microtubule dynamics classification" step, regardless of the value of the maximum gaps to close parameter. Is this an issue you've experienced before? All the data I'm working with are 2D. My working theory is that the problem may lie in plusTipCostMatCloseGaps.m. In line 180, for example, since all the entries of vz are NaN, the entries in velInst are also all NaN. There are some similar examples of z-components being NaN potentially throwing things off later on in the same function. Thanks for looking into this issue!

Hello,

Somewhat new to matlab, but I ran into a bug when I tried to use your overlayFeaturesMovie to generate a video of tracked cells (see below)

>> overlayFeaturesMovie(movieInfo, [1 239], 1, "movie.mov", [], 1, 1, [], [])

Error using fopen
First input must be a file name or a file identifier.

Error in MakeQTMovie>OpenMovieFile (line 507)
fp = fopen(MakeQTMovieStatus.movieName, 'wb');

Error in MakeQTMovie>AddFileToMovie (line 465)
OpenMovieFile

Error in MakeQTMovie (line 160)
[pos, len] = AddFileToMovie;

Error in movieInfrastructure (line 40)
MakeQTMovie addfigure

Error in overlayFeaturesMovie (line 333)
movieVar = movieInfrastructure('addFrame',movieType,dir2saveMovie,...

I tracked this bug back to line 507 in your MakeQTMovie.m file (as the bug specified). It looks like the MakeQTMovieStatus.movieName outputs an array of the full path as well as the file name. to get only the full path (as fopen needs) you should replace line 507 in the MakeQTMovie.m file with the following:

fp = fopen(MakeQTMovieStatus.movieName(1), 'wb');

This fixed the issue for me. However, it is possible different implementations of MakeQTMovieStatus.movieName do not require this fix. Therefore the fix may be more complex then the hacky workaround I found.

Hopefully that help!

Hi, I'm using the command-line version of the software and I've generated my own MovieInfo. When I run the scriptTrackGeneral.m, I've got the following error:
scriptTrackGeneral.m.zip
movieInfo.mat.zip

Error using  * 
Incorrect dimensions for matrix multiplication. Check that the number of columns in the first matrix matches the number of rows in
the second matrix. To perform elementwise multiplication, use '.*'.
 
Error in costMatRandomDirectedSwitchingMotionLink (line 219)
        stateVec = transMat(:,:,iScheme)*stateOld;
 
Error in linkFeaturesKalmanSparse (line 347)
            [costMat,propagationScheme,kalmanFilterInfoTmp,nonlinkMarker] = costMatFunc(...
 
Error in trackCloseGapsKalmanSparse (line 357)
    [~,~,kalmanInfoLink,~,linkingCosts] = linkFeaturesKalmanSparse(...
 
Error in scriptTrackGeneral (line 125)
[tracksFinal,kalmanInfoLink,errFlag] = trackCloseGapsKalmanSparse(movieInfo,...

I've found that the size of transMat(:,:,iScheme) is 44 and the size of stateOld is 31.
Can you help me with this issue? Many thanks!

I used the MovieSelectorGUI for analysis. As I tried to follow the visualization instructions and call the function plotCompTrack, an error occurred and gave me the following message:

Error using inputParserRetrofit/parse (line 190)
The value of 'trackedFeatureInfo' is invalid. It must satisfy the function: @(s)isstruct(s)||isnumeric(s).

Error in inputParserRetrofit/subsref (line 116)
[varargout{1:nargout}] = builtin('subsref',obj,S);

Error in plotCompTrack (line 82)
ip.parse(trackedFeatureInfo, varargin{:});

Is there anyone could bring me some insights on this?

At the same time, I also noticed that I was unable to open the .mov movie generated by the function. Is there anyone know what might be the cause of this?

I am using Mac. The U-track failed to load the library of mex. Can anyone help me with this issue?
identifier: 'MATLAB:mex:ErrInvalidMEXFile'
message: 'Invalid MEX-file '
Library not loaded: @loader_path/libmex.dylib

Hello everyone

I'm trying to use u-track 2.2.0 in matlab version R2022a but when I try to run it, several errors are showed up:

-- Step 1: Gaussian Mixture-Model Fitting

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

Error in robustMean (line 149)
medianData = nanmedian(data,dim);

Error in spatialMovAveBG (line 57)
[bgMeanFull,bgStdFull] = robustMean(imageLast5(nhoodIdx));

Error in detectSubResFeatures2D_StandAlone (line 369)
[bgMeanRaw,bgStdRaw] = spatialMovAveBG(imageLast5,imageSizeX,imageSizeY);

Error in detectMovieSubResFeatures (line 108)
movieInfo = detectSubResFeatures2D_StandAlone(movieParam, p.detectionParam, saveResults(i));

Error in Process/run (line 230)
obj.funName_(obj.getOwner(), varargin{:});

Error in packageGUI_RunFcn>userfcn_runProc_dfs (line 626)
userData.crtPackage.processes_{procID}.run(); % throws exception

Error in packageGUI_RunFcn>start_processing_movies_in_series (line 212)
userfcn_runProc_dfs(procID, procRun{iMovie}, handles); % user data is retrieved, updated and submitted

Error in packageGUI_RunFcn (line 157)
movieException = start_processing_movies_in_series(movieRun,handles,movieException,procRun);

Error in packageGUI_OpeningFcn>@(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)) (line 380)
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.

Can anyone help me with errors?

Dear authors,
Your manuscript "Piecewise-stationary motion modeling and iterative smoothing to track heterogeneous particle motions in dense environments" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5796444) states that "Our new motion model and estimator will part of the next release of the u-track platform at http://www.utsouthwestern.edu/labs/danuser/software/."
Is PMMS now available? I cannot find it in this repo, though I may have missed something.
Thanks in advance.

Hi, when I try to save the files after, steps of movie creation from. series of tiff files as mentioned in the pdf. I get the message below "Invalid or. detected object. please check your movie data? Movie data is not saved"

in the Matlab command windows the message is : matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)movieDataGUI('pushbutton_view_metadata_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

Please help to solve this problem because.

Thanks

Hi guys,i ran into this problem when loading .mov.I just don't know how to figure it out.
The program is running on win10,matlab2019b and it tells:
Java exception occurred:
loci.formats.MissingLibraryException: QuickTime for Java is not supported with a 64-bit JVM. Please invoke the 32-bit
JVM (-d32) to utilize QTJava functionality.
Can anyone help me with it?

It seems like I'm running into issues with particle detection.

My system specifications are the following:
Matlab version: 9.2.0.556344 (R2017a)
Operating System: Mac OS X Version: 10.15.2 Build: 19C57
Java VM Version: Java 1.7.0_75-b13 with Oracle Corporation Java HotSpot(TM) 64-But Server VM mixed mode

The main error that comes up after running through the detection and tracking steps is "Error using vertcat. Dimensions of matrices being concatenated are not consistent." Any help on this issue would be greatly appreciated!

Hi guys,
Awesome software and very cool that you implemented OMERO!
I can login to OMERO (5.4.10) through u-track but not able to load data.
The error message is as follows:

`Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Error in omeroDataSelectionGUI>omeroDataSelectionGUI_OpeningFcn (line 100)
groupIds = [groupIds1 groupIds2];

Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure),
varargin{:});

Error in omeroDataSelectionGUI (line 59)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});

Error in movieSelectorGUI>menu_omero_load_Callback (line 625)
userData.omeroDataFig = omeroDataSelectionGUI('mainFig',handles.figure1);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in movieSelectorGUI (line 61)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)movieSelectorGUI('menu_omero_load_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating Menu Callback.`

Does this look familiar?
Or would it be better to post this on OMERO message boards?

System specs:
4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) x86_64
MATLAB v. R2017b

Thanks!
Josh