Enrichment Score

I added a line to my properties file so that its output will be based on well not image. Here is the code:

group_SQL_Well+Plate = SELECT cellprofiler_DATABASE_Per_Image.ImageNumber, cellprofiler_DATABASE_Per_Image.Image_Metadata_Plate, cellprofiler_DATABASE_Per_Image.Image_Metadata_Well FROM cellprofiler_DATABASE_Per_Image

When I try to score all my images based on the grouping I defined, it crashes. By crashing I mean that it has been 24 hours and it is still at 99 percent.

When I ran the program using the score per image, it works perfectly fine and it gives me a table.

I work with python and I would like to use this cvs file in python. Since the program crashes when it is per well, What is the best way to combine enrichment scores? Since I have 9 image per well, and when I run it per image I get enrichment score per image. I would like to get enrichment score per well.


DISCLAIMER: I’m forwarding your question onto the people in the group who are more familiar with CPA performance; in the meantime what follows is my best advice:

Based on the description of the calculation of the enrichment score, it doesn’t look like there’s a way to easily linearly combine the different enrichment scores. By taking advantage of CPA’s own code (which is written in python) it should be possible for you to calculate your own per-well enrichment on your own data by re-creating the steps, but let’s start by just seeing if we can get CPA to do it for you.

One common thing to try to decrease freezing is editing your properties file so that check_tables is set to no. Can you give that a try?

What version of CPA are you running? Then I can check to see if there are any known bugs that match your issue.

Also, triple check your SQL query; since all of your data is in the same table, you can simplify it to

group_SQL_Well_Plate = SELECT ImageNumber, Image_Metadata_Plate, Image_Metadata_Well FROM cellprofiler_DATABASE_Per_Image