I’ve just downloaded the developer’s version of CP (CellProfiler.m: Revision: 7485 ) and run it with
MATLAB Version 126.96.36.1991 (R2008b)
Operating System: Linux 188.8.131.52.i686.7 #1 SMP PREEMPT Mon Aug 17 12:42:05 CEST 2009 i686
Java VM Version: Java 1.6.0_04 with Sun Microsystems Inc. Java HotSpot™ Client VM mixed mode
To get started, I was going to run the SBS pipeline on the example images provided, but I already ran into some problems:
- in the CalculateStatistics module, it seems that there is an error with the waitbar function as I get the following
There was a problem running the analysis module CalculateStatistics which is number 20.
Improper arguments for waitbar
waitbar in /amd/kronecker/2/package/matlab/matlabr2008b/toolbox/matlab/uitools/waitbar.m (249)
CPwaitbar in /amd/kronecker/2/package/cellprofiler/7522/CPsubfunctions/CPwaitbar.m (15)
CPcalculateStatistics in /amd/kronecker/2/package/cellprofiler/7522/CPsubfunctions/CPcalculateStatistics.m (91)
CalculateStatistics in /amd/kronecker/2/package/cellprofiler/7522/Modules/CalculateStatistics.m (162)
AnalyzeImagesButton_Callback in /amd/kronecker/2/package/cellprofiler/7522/CellProfiler.m (4505)
gui_mainfcn in /amd/kronecker/2/package/cellprofiler/7522/CellProfiler.m (6265)
CellProfiler in /amd/kronecker/2/package/cellprofiler/7522/CellProfiler.m (55)
I saw in the forum that there has been an issue with the waitbar function and the R2008b version before, but as far as I can tell the CPwaitbar function has now been updated accordingly so I don’t know how to fix that.
- When I choose to display the intermediate images for IdentifySecondary, and (after the image analysis is complete) change the Oulines:Secondary to e.g. Outlines:Primary and Secondary from the drop-down list, the image changes and always displays the corresponding image from cycle #1 which is very weird.
In general, I am not sure how to access the intermediate images from previous cycles if I’d like to examine the results of the pipleline on a few example images - under ‘windows’ in the main window, I can only click on the images generated in the currrent cycle…
I apologise if these are stupid questions!