Time sensitive: class about to start and CPA bug does not allow data visualization or analysis


#1

Dear Forum,
I finished CP analysis and database generation without issues.
CPA opens fine, however the plate viewer and other interfaces only show one well at a time instead of the 26 wells present in the database. I can select each well but I need the whole plate view for this exercise.
How do I select to see all wells simultaneously?
Also, any attempt to change how data is displayed or fetch gives me errors.
Below is the activity/error log and attached how the viewer looks.
I just added the properties file.

Thank you.

Logging level: DEBUG
Exception fetching new version information from http://cellprofiler.org/CPAupdate.html: HTTP Error 404: Not Found
[MainThread] Connecting to the database…
[MainThread] SQLite file: /Users/orourke/Desktop/DefaultDB.db
[MainThread] SELECT ImageNumber FROM MyExpt_Per_Image GROUP BY ImageNumber
[MainThread] Connected to database: /Users/orourke/Desktop/DefaultDB.db
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT DISTINCT src FROM link_tables_MyExpt_Per_Image_MyExpt_Per_Object
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] SELECT DISTINCT Image_Metadata_Well,Image_Metadata_Well FROM MyExpt_Per_Image WHERE Image_Metadata_Well != “” and Image_Metadata_Well IS NOT NULL
[MainThread] SELECT DISTINCT Image_Metadata_Well FROM MyExpt_Per_Image
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT DISTINCT Image_Metadata_Well FROM MyExpt_Per_Image
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well, AVG(MyExpt_Per_Image.ImageNumber)
FROM MyExpt_Per_Image
GROUP BY MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT DISTINCT src FROM link_tables_MyExpt_Per_Image_MyExpt_Per_Object
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] SELECT DISTINCT Image_Metadata_Well,Image_Metadata_Well FROM MyExpt_Per_Image WHERE Image_Metadata_Well != “” and Image_Metadata_Well IS NOT NULL
[MainThread] SELECT DISTINCT Image_Metadata_Well FROM MyExpt_Per_Image
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well, AVG(MyExpt_Per_Image.ImageNumber)
FROM MyExpt_Per_Image
GROUP BY MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well, AVG(MyExpt_Per_Image.ImageNumber)
FROM MyExpt_Per_Image
GROUP BY MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well
[MainThread] SELECT * FROM MyExpt_Per_Object LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Object)
[MainThread] SELECT * FROM MyExpt_Per_Object LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Object)
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT link FROM link_tables_MyExpt_Per_Image_MyExpt_Per_Object WHERE src=“MyExpt_Per_Object” AND dest=“MyExpt_Per_Image” ORDER BY ord
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT link FROM link_tables_MyExpt_Per_Image_MyExpt_Per_Object WHERE src=“MyExpt_Per_Object” AND dest=“MyExpt_Per_Image” ORDER BY ord
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT col1, col2 FROM link_columns_MyExpt_Per_Image_MyExpt_Per_Object WHERE table1=“MyExpt_Per_Object” AND table2=“MyExpt_Per_Image”
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT link FROM link_tables_MyExpt_Per_Image_MyExpt_Per_Object WHERE src=“MyExpt_Per_Object” AND dest=“MyExpt_Per_Image” ORDER BY ord
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT link FROM link_tables_MyExpt_Per_Image_MyExpt_Per_Object WHERE src=“MyExpt_Per_Object” AND dest=“MyExpt_Per_Image” ORDER BY ord
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT col1, col2 FROM link_columns_MyExpt_Per_Image_MyExpt_Per_Object WHERE table1=“MyExpt_Per_Object” AND table2=“MyExpt_Per_Image”
[MainThread] SELECT MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well, AVG(MyExpt_Per_Object.ImageNumber)
FROM MyExpt_Per_Object, MyExpt_Per_Image
WHERE MyExpt_Per_Object.ImageNumber = MyExpt_Per_Image.ImageNumber
GROUP BY MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well
[MainThread] SELECT name FROM sqlite_master WHERE type=“table” ORDER BY name
[MainThread] SELECT * FROM link_columns_MyExpt_Per_Image_MyExpt_Per_Object LIMIT 1
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] SELECT * FROM link_columns_MyExpt_Per_Image_MyExpt_Per_Object LIMIT 1
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Nuclei_Location_CenterMassIntensity_X_DNA
FROM MyExpt_Per_Image
GROUP BY MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well
[MainThread] SELECT * FROM MyExpt_Per_Image LIMIT 1
[MainThread] PRAGMA table_info(MyExpt_Per_Image)
[MainThread] SELECT MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Nuclei_Location_CenterMassIntensity_X_DNA
FROM MyExpt_Per_Image
GROUP BY MyExpt_Per_Image.Image_Metadata_Well, MyExpt_Per_Image.Image_Metadata_Well

DefaultDB_MyExpt.properties (6.2 KB)


#2

For posterity, in case anyone ever ends up having this issue again- the issue ended up being incorrect metadata specification of the Plate.