Error while processing ExportToDatabase message

I’m having trouble with the following error when running through the ExportToDatabase module:

Error while processing ExportToDatabase
numpy boolean subtract, the - operator, is deprecated, use the bitwise_xor,the ^ operator, or the lgical_xor function instead.

Can anyone help me figure out what I need to change please?

Hi @Laura_B,

Would you be able to upload a copy of the pipeline so that we can figure out which settings are causing this? It’d also be handy to know which version of CellProfiler you’re running.

Also, does this error actually stop the pipeline? If it doesn’t you should be fine to continue.



I’ve uploaded the pipeline, I’m using CellProfiler version 3.1.9.
If I click continue on the error the pipeline continues but I have to click this for each image set.

LauraGFP intensity.cpproj (696.3 KB)

So far I’ve unfortunately not been able to replicate this on my end, although I’ve been using a sample data set. It does sound like this is a bug, would you be able to provide the full error message sequence from the console? If running Windows this should appear in the black console window, if you’re on Mac you might need to launch CellProfiler from the terminal. You’ll be looking for a “Traceback” which will help us figure out which command is causing this.

Alternatively if you could upload some of the images needed by the pipeline (and the associated metadata file) I can investigate this further on my end.


N2 PICO plate layouts2.csv (1.3 KB)
Sorry for the delay. I’ve uploaded a text file with the error message sequence, along with a few image sets and with the metadata csv file. I’ve also uploaded the pipeline again because I changed the metadata matching, although this hasn’t solved the issue.

Laura_n_2_A01_sx_1_sy_1_w1.tif (7.7 MB) _n_2_A01_sx_1_sy_1_w1_Probabilities_1.tiff (2.5 MB) _n_2_A01_sx_1_sy_1_w2.tif (7.7 MB) _n_2_A01_sx_1_sy_1_w2_Probabilities_0.tiff (4.0 MB) _n_2_A01_sx_1_sy_1_w2_Probabilities_1.tiff (3.8 MB) _n_2_A01_sx_1_sy_2_w1.tif (7.7 MB) _n_2_A01_sx_1_sy_2_w1_Probabilities_1.tiff (2.6 MB) _n_2_A01_sx_1_sy_2_w2.tif (7.7 MB) _n_2_A01_sx_1_sy_2_w2_Probabilities_0.tiff (4.3 MB) _n_2_A01_sx_1_sy_2_w2_Probabilities_1.tiff (4.1 MB) Error from console .txt (7.8 KB) N2 PICO plate layouts2.csv (1.3 KB)

GFP pipeline.cpproj (115.3 KB)

Hi @Laura_B,

Thanks for uploading that, I’ve taken a look and found the error. It looks like the “write image thumbnails to database” option currently isn’t working with binary images (the result from the threshold module). I’ll work on fixing this for the next release of CellProfiler, but for now you should be able to get it working if you disable writing thumbnails to the database for the image produced by the threshold module.

Great, yes that works now thank you!

The only problem I’m having now is that not all of the metadata from my metadata csv. is being included in the final output spreadsheet, some values such as my Metadata_promoter column all just say nan. Do you have any idea what I am doing wrong?

Thank you,

Ideally metadata values need to be shared between all images in an image set. The ‘nan’ that you see is typically because when there are multiple entries CellProfiler wants to average them and can’t. If you check your metadata, does each image in a set have the same Metadata_promoter column? It may help if you could screenshot the metadata table.

Yes, each image set has the metadata, here’s the screenshot:

Thanks, I understand that you’re importing metadata from the CSV, but when you ‘update’ metadata in CellProfiler I’d like to see what the table within the software on the Metadata module actually produces?

Here is a screenshot of the table after I hit update:

It looks like Metadata_Promoter isn’t being extracted at all there?

No, do you know what I’m doing wrong?

In your pipeline it looks like you’ve set the Metadata module up to match the CSV’s ‘PlateID’ with ‘Plate’ and ‘Well’ with ‘Well’. For this to work the contents of each column must be able to be matched. In your CSV ‘Metadata_PlateID’ is numeric, but the Plate column that it’s matching with in the screenshot above has everything set to ‘TimePoint_5’. I believe this is the problem, the matching template needs to produce a single match for each row.

Thank you! I noticed that I had originally named my wells differently but not the PlateIDs. It includes all of the metadata in the table now.

Thank you so much!