Value Error: The truth value of any array with more than one element is ambiguous



Hi there,

First of all, I am a new user both in CellProfiler and in the forum and although I have used the search function in the upper right corner to see whether any other user has had this same problem I have not find anything. So, given that the issue is already resolved, please let me know.

As I have said I am a new user of CellProfiler and I have high hopes that this “value error” is due to some kind of mistake made by me. So, the thing is that I am trying to process sets of three images (3D images) that I have converted to tiff (by splitting the channels) in Fiji. To this end, I have been following your 3D tutorial, modifying the pipeline to our needs. We are a laboratory that is using for the first time CellProfiler (previously using Fiji) mainly because of the new 3D features of the 3.0 version, and we would really appreciate your help in solving this issue. Again, if this issue has already been resolved previously I will be very grateful if you could direct me to the post. I attach the images that we are trying to process and the (modified) pipeline.

The outcome of the Image analysis is CellProfiler windows opening and closing fast and the abovementioned (in the title) message. Also, we do not obtain any output. I would really appreciate your help as our closer colleagues do not have enough expertise with 3D CellProfiler and we would like to set this pipeline to analyse 3D images of skin topography. Thank you very much for your help, and should you require more information do not hesitate to ask. (5.3 MB)

Value error pipe.cppipe (20.2 KB)


Sorry, for some reason it did not let me add the three images. Here’s the link to my dropbox. Thank you very much again.



Thanks for the images and pipeline. I get the same issue as you and I don’t think it is due to a mistake by you as you hoped and may possibly be a bug.

I have reported it as an issue here: and suggest you keep an eye on the thread to see how it progresses. Sorry for the inconvenience!