Names and Types Error

Dear All,

I am trying to create a pipeline to quantify double positive cells with nuclear and cytoplasmatic staining using CP and CP analyst. After loading the images in CP, and extracting the metadata, the pipeline crashes in NamesAndTypes. These are the two different errors that I get. The difference come when I change some parameters in the “Regular Expression” box from “Metadata”. - because I thought the problem might come from this field.

  • Exception in CellProfiler core processing
    Traceback (most recent call last):
    File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/moduleview.py”, line 2416, in
    File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/moduleview.py”, line 2423, in on_predicate_changed
    File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/settings.py”, line 2695, in parse
    File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/settings.py”, line 2746, in parse_token
    ValueError: List required in current context

Traceback (most recent call last):
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/moduleview.py”, line 2416, in
File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/moduleview.py”, line 2426, in on_predicate_changed
TypeError: object of type ‘DoesPredicate’ has no len()

This pipeline is a shorter version of a friend’s one, which works, however, neither my friend nor I have been able to spot the problem.

Many thanks,

Images
4channels.zip (474.7 KB)
Pipeline
NG2_O4_Olig2_test2.cpproj (141.4 KB)

Hi,

This is an occasional issue that crops up when pipelines go back and forth across CP versions; I suspect you and your friend may have different versions installed (if you could let me know your respective versions, OSes, etc that’d actually be great). The fix is described here; I’ve applied it to this particular pipeline and re-uploaded it.

NG2_O4_Olig2_test2.cppipe (20.1 KB)

Also, if you could do the following, this would be great and help us finally figure out why this issue is happening and hopefully fix it (we’ve never been able to fully trace the before-and-after versions to figure out what goes wrong between them):

  • Get the pipeline again from your friend
  • Upload exactly the copy they sent you to the forum without opening it.
  • Open it in your version of CP, see if the issue still happens; if so, save it with a slightly different name (like XXX_converted).
  • Upload the converted version.

Hi.
Thank you for your rapid response, I followed the instructions of the link that you mentioned and, it works now - many thanks.

Regarding to your requests:
my CP version is 2.2.0 (rev 9969f42), OS, El Capitan, 10.11.06, 8 gb
my friend’s CP version is 2.2.0 (rev 9969f42), OS Yosemite, 10.10.05, 8 gb.

The original file (without opening it)
MBP_PI_CD11b.cpproj (2.4 MB)

The problem still happens so, this is the other file,
XXX_converted.cpproj (152.8 KB)

Hope this helps and many thanks again,

That was TREMENDOUSLY helpful actually, it helped us trace this back to a previously known issue which sets us up on the path to retracing why the original fix didn’t quite work and letting us fix it for real. Thanks again!