Yeast example: problems

Hello,
I just installed CellProfiler Beta (V9722) on an ol’ Win2K-SP4-pro machine (AMD sempron 2800, 1.6 Go RAM).
I tried to run the Yeast example image treatment, and encounter problems.

A) First, the as-is pipeline “ExampleYeastColonies_BT.cp” on the yeast example image did hit the wall of “memory error” (bug already reported on this forum).

B) I then removed the display windows on all intermediate steps, and the pipeline did finish, with the outlines of the colonies stored in the result image.
However, I do not have acess to any “result” data (no excel compatible file appears to be created) What is the reason ? should a modification be included in the example pipeline ?

C) I then restored the window display but only on MeasureObjectSizeShape, and ClassifyObjects (the 2 occurences); I got some numbers by the way, what are the units used !? ], could save to a pdf file (MeasureObjectSizeShape); also I got low-resolution plotted histo’s. Fine, but still not able to get exportable data for example for the distribution of colony size. Some suggestion ?

D) I went to explore (using MatLab R2007a) the mat files created. Did not find much usefull data in those (other than correct execution flags). {…where is the beef :confused: ? }

Thank you for your help !

Unfortunately, we have not been able to replicate the lack of data that you describe. You should have gotten a couple of comma-separated (.csv) files in the default output folder, the same folder that the outline image is stored; one would have ‘Image.csv’ appended to the name, the other with ‘Colonies.csv’. Were these files not produced?

As an aside, the morphological (MeasureObjectSizeShape) data are measured in terms of pixel units. Length-based measurements are in pixel units, area-based measurements are in pixel^2, and others are unitless.

Similarly, the handles structure in the DefaultOUT.mat file should contain the relevant measurements, in the fields handles.Measurements.Image and handles.Measurements.Colonies. Can you tell us whether these fields were produced in your output .mat file?

Regards,
-Mark

Hello,
thanks for your feedback.

I get none of those csv files; I only get the oulined image.


I actually did another test, … and found what was the problem ! ! !
I was actually running the pipeline via “start test run / run”; this does not create the excel files, nor does the matFile contain measurements, even though the histo are displayed at the end.

I realized finally that the appropriate way to start, was via the** “analyse image” button**.
This did give the excel files (and also the mat file now contains measurements)

Fine, my problem is solved ! :smiley:

found now in the matFile:


handles.Measurements.Colonies.Intensity_StdIntensityEdge_SubtractedRed,
handles.Measurements.Colonies.Classify_red,handles.Measurements.Colonies.AreaShape_Orientation,
handles.Measurements.Colonies.Intensity_MassDisplacement_SubtractedRed,
handles.Measurements.Colonies.Intensity_MeanIntensityEdge_SubtractedRed,
handles.Measurements.Colonies.Intensity_IntegratedIntensityEdge_SubtractedRed
,handles.Measurements.Colonies.Classify_white,
handles.Measurements.Colonies.Intensity_UpperQuartileIntensity_SubtractedRed,
handles.Measurements.Colonies.AreaShape_Eccentricity,
handles.Measurements.Colonies.Intensity_LowerQuartileIntensity_SubtractedRed,
handles.Measurements.Colonies.Intensity_MeanIntensity_SubtractedRed,
handles.Measurements.Colonies.AreaShape_Solidity,
handles.Measurements.Colonies.Intensity_IntegratedIntensity_SubtractedRed,
handles.Measurements.Colonies.AreaShape_FormFactor,
handles.Measurements.Colonies.Intensity_MaxIntensityEdge_SubtractedRed,
handles.Measurements.Colonies.Classify_tiny,
handles.Measurements.Colonies.Classify_small,
handles.Measurements.Colonies.Intensity_MinIntensity_SubtractedRed,
handles.Measurements.Colonies.AreaShape_MajorAxisLength,
handles.Measurements.Colonies.AreaShape_Perimeter,
handles.Measurements.Colonies.Intensity_StdIntensity_SubtractedRed,
handles.Measurements.Colonies.Intensity_MinIntensityEdge_SubtractedRed,
handles.Measurements.Colonies.Number_Object_Number,
handles.Measurements.Colonies.AreaShape_Extent,
handles.Measurements.Colonies.AreaShape_MinorAxisLength,
handles.Measurements.Colonies.Classify_large,
handles.Measurements.Colonies.Intensity_MaxIntensity_SubtractedRed,
handles.Measurements.Colonies.AreaShape_EulerNumber,
handles.Measurements.Colonies.AreaShape_Area,
handles.Measurements.Colonies.Location_Center_X,
handles.Measurements.Colonies.Location_Center_Y,
handles.Measurements.Colonies.Intensity_MedianIntensity_SubtractedRed

Thanks for posting what you found out. Since we’re trying to make the new release of CP as user-friendly as possible, we’ll take your user-feedback into account. In the meantime, we hope that CP will suit your needs!
-Mark