Display platemap module problem


Hi,
I’m trying to read metadata from filenames and want to use them to display a platemap of my 96 well plate.
My problem is that i always get a pipeline error like this:

Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 932, in do_step
File “cellprofiler\modules\displayplatemap.pyc”, line 214, in run
File “cellprofiler\gui\cpfigure.pyc”, line 1363, in subplot_platemap
File “cellprofiler\gui\cpfigure.pyc”, line 1422, in format_plate_data_as_array
ValueError: substring not found

I imported the metadata from the filename like this:


My DisplayPlatemap options are these:


Does anyone has have a suggestion what I did wrong?

Thanks,

spu

Hi spu,

I believe the problem is that the 96- and 384-well plate settings assume the standard format of the rows being named A-H (96-well) or A-P (384-well), and the columns named 01 - 08 (96-well) or 01 - 24 (384-well); your plates do not seem to be named this way. A workaround would be rename the files accordingly, either using a 3rd-party program or CellProfiler’s RenameOrRenumberFiles module. Unfortunately, this is not stated explicitly in the help for the DisplayPlatemap modiule; we will annotate this fact for a future release.

Regards,
-Mark

thank you mark,
now the rekongnition of the well works fine.
but there ist still a problem.
i’ve got a square of four areas per well. and the results should be averaged in the platemap.
the first cycle runs without an error, but when it comes to the second one the following error occurs:

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\displayplatemap.pyc”, line 195, in run
File “numpy\core\fromnumeric.pyc”, line 2309, in mean
File “numpy\core\fromnumeric.pyc”, line 37, in _wrapit
File “numpy\core\numeric.pyc”, line 261, in asarray
ValueError: setting an array element with a sequence.

do yo have an idea?
spu

Hi,

Would you be able to post your pipeline plus the images that constitute the first well, so we can diagnose the issue?
-Mark