Cell profiler errors

Hi there

I have created a pipeline to analyse some images stained by in situ hybridisation. The staining pattern is a ‘salt and pepper’ type pattern, with some dots of stain in a mostly unstained background. I wish to count these dots of expression, and have created a pipeline to load images>identify primary objects> measure object size and shape> export to a spreadsheet

I have two questions:

  1. I don’t really need all the data about the identified object, just a count would be fine, is there a better way to do this that MeasureObjectSizeShape?
    2)The pipeline works fine for a single test image, but once I try and get it to work through a folder of about 10 images, I get an error- this is the detail:
    Traceback (most recent call last):
    File “cellprofiler\pipeline.pyc”, line 309, in run
    File “cellprofiler\modules\identifyprimaryobjects.pyc”, line 800, in run
    File “cellprofiler\modules\identify.pyc”, line 394, in add_threshold_measurements
    File “cellprofiler\cpmath\threshold.pyc”, line 627, in sum_of_entropies
    File “cellprofiler\cpmath\smooth.pyc”, line 36, in smooth_with_noise

Hopefully someone can be of assistance!

Hi Julie,

IdentifyPrimaryObjects outputs a count as a result; no further modules needed.

Do you get this error if you select Windows > Hide all windows on run from the main menu?