Dear CellProfiler developers,
After careful manual inspection I believe to have encountered a bug/error with possibly large consequences.
in my pipeline I do (among other stuff) the following:
- I create a binary image of my original image
- I feed this image to the “IdentifyPrimaryObjects” module using the “manual” thresholding method, with threshold set to 0.1
- I save the objects myobject as png image
- I save the data in hdf5, in the dhf5 file: foo/Image/Count_myobject every now and then the number of myobject objects is way lower or zero while this is not the case in the original image and saved myobject png images.
I use the latest stable 2.1 CP release on windows 7
The hdf5 files are too large to upload here (several GB per hdf5 file), The pipeline uses some home made modules which I could send after permission from licence holder. However the output of these home parts is a binary image so I don’t think the problem is in this direction.
I attached one of the pipelines where this is happening and also the corresponding images. The image where the count is suddenly low is: D13_2 in the 11th image/ time point channel 1: 20130922 tp53 tiffsxy112c1t11.tif
My concern with this is that the objects are lost - and also all derived objects e.g. secondary objects seeded from these primary objects and corresponding measurements. I also have examples where the image object count was zero - but nothing seemed wrong with the primaryobjects images/ original images.