Load Images, deltavision

Hi all,

I’m trying to correctly load and group images from a deltavision DV file. I’ve attached the pipeline I’ve been using although I’m not sure it will be much help without the images file (which is 2.7 GB).

The DV file represents a single well of a 96-well plate where I’ve imaged 16 fields per well taking 20 z slices for 4 channels.

Really, I’m just playing around right now, but as a test, the pipeline I have just makes a maximum intensity projection of the DNA images and saves the file.

When I run the pipeline, I’m getting the following error:

Traceback (most recent call last):
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/pipeline.py”, line 2094, in prepare_run
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/modules/namesandtypes.py”, line 753, in prepare_run
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/modules/namesandtypes.py”, line 1209, in create_imageset_dictionary
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/measurements.py”, line 361, in setitem
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/measurements.py”, line 805, in add_measurement
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/hdf5_dict.py”, line 486, in setitem
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/hdf5_dict.py”, line 577, in setitem
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/hdf5_dict.py”, line 54, in new_setitem
File “h5py/_hl/dataset.pyc”, line 415, in setitem
File “h5py/_hl/selections.pyc”, line 94, in select
File “h5py/_hl/selections.pyc”, line 261, in getitem
File “h5py/_hl/selections.pyc”, line 512, in _handle_simple
File “h5py/_hl/selections.pyc”, line 553, in _translate_slice
ValueError: Zero-length selections are not allowed

I’ve attached the pipeline I’m using and screen shots to show how I’ve grouped the images. I’ve loaded the images based on the header metadata and first defined images by ‘C’, then made image sets by ‘Series’ and ‘Z’. Here, there series represents each field. Last I grouped the images by Series.








Any thoughts?

Thanks.

JT
DV_test.cppipe (5.64 KB)

HI all,

A small update. I was actually patient enough to let the pipeline run and it looks as though it’s generating the proper images despite the error when starting the pipeline.

JT

Any chance you might be able to upload a smaller version of the image file, so we can take a look to see if it’s a bug we can fix?
-Mark

I am actually experiencing the exact same problem. As was posted above, if I let it run, everything seems to be fine. Was there ever any update on why this happens/ how I can prevent it in the future?

Hi @ kMichaels,

To my knowledge, we don’t have a DV file here to test. Can you upload one here, or link it in, say, Dropbox?

Thanks,
David