Measure intensity in different parts of cilia

I would like to measure the intensity of different parts of the cilia. In ch1 I have a stain that I use to detect and segment the cilia. From this one I use the intensity in ch2 to measure intensity of the cilia. I have made the find primary objects for ch2 dependent on the objects found in ch1. However what I really want is to divide the length of the cilia in 10 equal parts so I can measure intensity in these during different conditions. Some conditions will give high signal in the tip and some won’t. Could you please help me with this pipeline? I tried to add two images but it would not up-load.
Best regards
fredrik
andy_cilia.cpproj (588.8 KB)

I will take a look, but first, do you recall what was the error/issue with uploading the images? You should be able to do this, but the Discourse forum is still a little new to us, so we may need to configure something. What kind of images are they? What file extension? Thanks.

Without the images, it’s hard to start on this. Please try and upload again, or at last resort you can use e.g. Dropbox or Google Drive.

But to break the cilia into 10 equal parts and measure anything about them like intensity, perhaps the best way would be to use MeasureRadialDistribution which creates annuli around a central object, typically a nucleus, but perhaps you could use the base of where the cilia attach as the “seed”? They would only be small segments of the ‘annuli’, but that would be fine. Again, we’d need to see the images to help further.

https://dl.dropboxusercontent.com/u/79782377/DS%202-1-Image%20Export-245_c2.tif
https://dl.dropboxusercontent.com/u/79782377/DS%202-1-Image%20Export-245_c1.tif

hello David
I tried again but it does not upload the images. I did add them via dropbox instead. These are saved as tif’s.
Thanks for helping me.
Best regards
Fredrik

Hello David
I think the problem was easy, i had changed the location of the images but not saved the pipeline. i think that was the problem.
Best regards
Fredrik

Hello David
there seems to be an error, this is the message. I have also added a modified pipeline.Would you make changes to this pipeline?
andy_cilia.cpproj (580.9 KB)

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 2094, in prepare_run
File “cellprofiler\modules\namesandtypes.pyc”, line 753, in prepare_run
File “cellprofiler\modules\namesandtypes.pyc”, line 1209, in create_imageset_dictionary
File “cellprofiler\measurements.pyc”, line 361, in setitem
File “cellprofiler\measurements.pyc”, line 805, in add_measurement
File “cellprofiler\utilities\hdf5_dict.pyc”, line 486, in setitem
File “cellprofiler\utilities\hdf5_dict.pyc”, line 577, in setitem
File “cellprofiler\utilities\hdf5_dict.pyc”, line 54, in new_setitem
File “h5py\highlevel.pyc”, line 1265, in setitem
File “h5py\selections.pyc”, line 94, in select
File “h5py\selections.pyc”, line 261, in getitem
File “h5py\selections.pyc”, line 512, in _handle_simple
File “h5py\selections.pyc”, line 553, in _translate_slice
ValueError: Zero-length selections are not allowed