Error shows matplotlib-problem (windows 10)



Dear all,

Does anyone have an idea where this error comes from?


Since I had a problem after my last Java update (could not open cellprofiler anymore), I uninstalled cellprofiler 3.0.0 and I installed the newest cellprofiler release. Now I can open cellprofiler, but as soon as I start the first step in the testmode with my images (which is the ColorToGray module in my pipeline), I receive the error. I’m happy for any help!!!
Some version informations:

java version “1.8.0_181”
Java™ SE Runtime Environment (build 1.8.0_181-b13)
Java HotSpot™ 64-Bit Server VM (build 25.181-b13, mixed mode)

jdk1.8.0_171 and jre1.8.0_181 in “C:\Program Files\Java”

cellprofiler 3.1.5 in “C:\Program Files\CellProfiler\CellProfiler.exe”

computer: desktop, windows 10, 64-bit

Thanks a lot, Nadine


Hi Nadine,
Can you upload your pipeline and a sample image set so we can try to reproduce this? Thanks!


Dear bcimini,
Thanks for your fast reply! My pipeline (which was working fine the last months…) is here (unfortunately, I can only upload pictures as a new user):

Here is also the beginning of the pipeline as a text from a former analysis with cellprofiler 3.0.0 (some parts are shortened, indicated with […]):

Pipeline_Pipeline,"CellProfiler Pipeline:

Images:[module_num:1|svn_version:‘Unknown’|variable_revision_number:2|show_window:False|notes:\x5B’To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.’\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Filter images?:Custom
Select the rule criteria:and (file doesnot startwith “”."")

Metadata:[module_num:2|svn_version:‘Unknown’|variable_revision_number:4|show_window:False|notes:[…].’\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Extract metadata?:Yes
Metadata data type:Text
Metadata types:{}
Extraction method count:1
Metadata extraction method:Extract from file/folder names
Metadata source:File name
Regular expression to extract from file name:^(?P.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})s(?P\x5B0-9\x5D)w(?P\x5B0-9\x5D)
Regular expression to extract from folder name:(?P\x5B0-9\x5D{4}
Extract metadata from:All images
Select the filtering criteria:and (file does contain “”"")
Metadata file location:
Match file and image metadata:\x5B\x5D
Use case insensitive matching?:No

NamesAndTypes:[module_num:3|svn_version:‘Unknown’|variable_revision_number:8|show_window:False|notes:[…].’\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Assign a name to:All images
Select the image type:Color image
Name to assign these images:AnalyseA
Match metadata:\x5B\x5D
Image set matching method:Order
Set intensity range from:Image metadata
Assignments count:1
Single images count:0
Maximum intensity:255.0
Process as 3D?:No
Relative pixel spacing in X:1.0
Relative pixel spacing in Y:1.0
Relative pixel spacing in Z:1.0
Select the rule criteria:and (file does contain “”"")
Name to assign these images:DNA
Name to assign these objects:Cell
Select the image type:Grayscale image
Set intensity range from:Image metadata
Maximum intensity:255.0

Groups:[module_num:4|svn_version:‘Unknown’|variable_revision_number:2|show_window:False|notes:[…].’\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Do you want to group your images?:Yes
grouping metadata count:1
Metadata category:FileLocation

ColorToGray:[module_num:5|svn_version:‘Unknown’|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:AnalyseA
Conversion method:Combine
Image type:RGB
Name the output image:AnalyseB
Relative weight of the red channel:1.0
Relative weight of the green channel:1.0
Relative weight of the blue channel:1.0
Convert red to gray?:Yes
Name the output image:OrigRed
Convert green to gray?:Yes
Name the output image:OrigGreen
Convert blue to gray?:Yes
Name the output image:OrigBlue
Convert hue to gray?:Yes
Name the output image:OrigHue
Convert saturation to gray?:Yes
Name the output image:OrigSaturation
Convert value to gray?:Yes
Name the output image:OrigValue
Channel count:1
Channel number:Red\x3A 1
Relative weight of the channel:1.0
Image name:Channel1

and these are some sample pictures:

Thanks again, Nadine


Hi, I’m getting the same Error message after updating to CellProfiler 3.1.5.

Did you solve the issue ?


Hi Nanny,

Thanks for reporting this bug. Could you please check if closing eyeball on running the pipeline helps since it is a display error. Meanwhile I opened this issue on GitHub.



Could you please upload your pipeline again?


Hi, I cannot reproduce this problem in CellProfiler version 3.1.5. Can you please check if you have selected Image type in Names and Types as color image?