Error converting to GrayScale


I’m trying to convert a four channel .TIF file from Colour to Gray and keep getting the following error message:

Error while processing ColorToGray:
index 3 is out of bounds for axis 2 with size 3
Do you want to stop processing?

Any ideas how I can resolve this issue. I would put the information from the command window but since installing CellProfiler 3.1.5. this no longer appears (if anyone could also tell me how to get this back that would be much appreciated).


Can you upload the pipeline and image?

I also encountered the same error. Please find attached the image and the pipeline.PCE-TDTG-T6_CRE _GFP_TDtomato_CC1_olig2_caudal_009_slice21.tif (2.0 MB)
PCE-TDTG-T6_CRE _GFP_TDtomato_CC1_olig2_rostral_006_slice16.tif (2.0 MB)
four-channel-coloc-find-objects.cpproj (595.6 KB)

Hi @raaghavi,

When I download these images they are both single channel TIFs. Therefore I think that the above error shouldn’t really apply?

Could you elaborate more on your problem?


Hi @lmurphy,

The metadata states this is a 4 channel image.
These are example images i got from the internet. I am using them to test my pipeline. I am developing a pipeline to analyse and count 4 channel fluorescent images (DAPI to detect nucleus and 3 fluorescent labelled intracellular biomarkers). I want to count the number of cells with the markers and also measure the intensity of each fluorescent signal.
Can you please tell me if my pipeline will work ?

Thank you,