CPA classifier

Hello Mark,

I have a problem by the classification of the positive cells in my experiment. After the measurement by CP2.0, I export the results into a database. When I try to fetch the cells in the classifier module of CPA, I get only black images. (The situation is similar to a previous problem: viewtopic.php?f=12&t=1668&p=6575&hilit=DBException%3A+ERROR+error%2C+fetching#p6575).

The appearing error message is the next:

An error occurred in the program:
DBException: ERROR: Database query failed for connection “MainThread” and failed to reconnect
Query was: “SELECT Single droplets_Location_Center_X, Single droplets_Location_Center_Y FROM Per_Object WHERE (ImageNumber=5 AND ObjectNumber=3614)”
First exception was: no such column: Single
Second exception was: ERROR: Database query failed for connection “MainThread”
Query was: “SELECT Single droplets_Location_Center_X, Single droplets_Location_Center_Y FROM Per_Object WHERE (ImageNumber=5 AND ObjectNumber=3614)”
Exception was: no such column: Single

Traceback (most recent call last):
File “imagetile.pyc”, line 119, in OnDClick
File “dbconnect.pyc”, line 633, in GetObjectCoords

I have tried to change the name of the column “Location_Center_X” to “Single” or to “Single droplets_Location_Center_X” and I did the same with “Location_Center_Y”. Unfortunately it did not work. What should I change?
In the attachment you can find the files about one single analysis.

Thank you for your help in advance.

Best regards,

LD pipeline 16072012.cp (17.6 KB)
Proba.rar (9.6 MB)

Hi Gergö,

I believe that the problem lies in that the object name should only have letters, numbers or underscores; no spaces. Such a name is fine in CellProfiler but not for CellProfiler Analyst.

Hope this helps!

Hello Mark,

Thank you for your answer. I have changed all the names of the identified objet’s but then I faced a new problem. When I start to classify the cell, again black images appearing with an error message (see atachment). Do I may need to change someting in the PROPERTIES file?



Hi Gergo,

I believe the issue you are encountering is because you are storing object measurements for which there is not a one-to-one correspondence between the object labels; that is, for every nuclei, there is not one SingleDroplet. For more details on the implications of this, see this post: NULL values in per_object.

The reason why this is giving a problem in your case is that if you having CPA fetch Nuclei (which I couldn’t tell for certain since I don’t have the properties file, but I can infer from the error message), there will be rows in the per-object database for which the x,y coordinates are NULL, because there are so many more SingleDroplets per image. CPA can’t find an object for which there are no coordinates, and so it fails.

The workaround is similar to that of the post mentioned above: Export the measures into separate per-object tables and use CPA on only one at time. Since you are using RelateObjects to relate the SingleDroplets to the Nuclei, the SingleDroplet measurements will still be in the Nuclei table, but just aggregated per-nuclei such that it will be one-to-one (1 nuclei measure to 1 aggregate droplet measure).


A post was split to a new topic: CPA “No Such Column” Error