Display platemap module

Hello,

I have been experimenting with the DisplayPlateMap module with little success due to the following error:

Traceback (most recent call last):
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/pipeline.py”, line 306, in run
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/modules/displayplatemap.py”, line 199, in run
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/gui/cpfigure.py”, line 1176, in subplot_platemap
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/gui/cpfigure.py”, line 1235, in format_plate_data_as_array
ValueError: substring not found

I’m not sure if this is a bug or an error on my part. I have sent the error report to you and I have attached my pipeline and a screenshot if that’s of any use. Is there something I’m doing wrong which could be rectified?

Many thanks for your help and patience!

Barry
Pipeline.cp (7.4 KB)


First, in loadimages you need to make sure that you are extracting the relevant metadata, which includes 2 things:

  1. a plate identifier
  2. a well identifier
    eg: if your filenames look like this
    ASDF_0925_0501110405_A01f00d0.png
    ASDF_0925_0501110405_A02f00d0.png

    ASDF_0925_0501110406_A01f00d0.png
    where the green is your plate name and the red is you well name, then a regular expression like this would pull them out for each filename:

…this is well documented in the loadimages help, and for all I know, you are doing it correctly.

What is definitely not correct however is in your display_platemap settings you are specifying filename_DAPI for the plate metadata and filename_transferrin for the well metadata. What you should be selecting here are Metadata_Plate and Metadata_WellName where Plate and WellName are the names that you gave to the substrings you extracted from the filenames in loadimages.

Let me know if anything isn’t clear. It would be helpful to see an example image filename and your configurations for loadimages.

If a file name contain spaces can we write a regular expression for it.

My imaging software has generated all the images with a file name of format
File name:
LOPAC 1-4, HCT116 WT_A2_1_2010y09m21d_16h00m

I am unable to write a regular expression for this. I only want 2 fields, plate name (Lopac 1-4) and well number (A2).
Kindly help me in this regard.

Regards,
Obaid

Spaces shouldn’t be a problem… I’m going to PM / email you a re that should work. (Unfortunately the forum mistakes the code for syntax and blows up.)

-Adam

Thanx Adam, i have fixed it :smile: