Cell Analyst Data Export Question

I have properly configured Cell Analyst. I would like to be able to export the the data. Primarily, I want to be able to use the Classifier to remove anomalous objects and then allow me to export the “accepted” objects into Microsoft Excel. Is this possible or is the only thing that Cell Analyst can export is images of the graphs?

Thanks for a great software.

-Michael

Indeed you can! Calassifeid Object Table

This method allowed me to save a summary of the number of accepted objects and unaccepted objects per image. Is there any way to export the area or mean of the accepted cells? I want to use Classifer as a filter and then examine the data gathered by Cell Profiler of the accepted cells in Excel.

Thank you for your help!

-Michael

Yes, we added a setting in the properties file for just this sort of functionality. In the properties file, add the feature column you want summed:

> # ======== Area Based Scoring ========
> # OPTIONAL
> # You may specify a column in your per-object table which will be summed and
> # reported in place of object-counts when scoring.  The typical use for this
> # is to report the areas of objects on a per-image or per-group basis.

> area_scoring_column = <NAME OF COLUMN IN DATABASE>

If this is not what you need, and you want e.g. each individual object’s area, then you’ll have to do a SQL query directly on the database. This query does that for object size:

SELECT MyTable_Per_Image.Image_Metadata_Plate,
MyTable_Per_Image.Image_Metadata_Well, 
MyTable_Per_Image.Image_Metadata_Site, 
MyTable_Per_ParasitesGood.ParasitesGood_Location_Center_X, 
MyTable_Per_ParasitesGood.ParasitesGood_Location_Center_Y, 
MyTable_Per_ParasitesGood.ImageNumber, 
MyTable_Per_ParasitesGood.ParasitesGood_Number_Object_Number, 
MyTable_Per_ParasitesGood.ParasitesGood_AreaShape_Area, 
MyTable_Per_ParasitesGood_Classes.class 
FROM MyTable_Per_ParasitesGood, MyTable_Per_Image, MyTable_Per_ParasitesGood_Classes 
WHERE (MyTable_Per_Image.ImageNumber=MyTable_Per_ParasitesGood_Classes.ImageNumber)
AND  (MyTable_Per_Image.ImageNumber=MyTable_Per_ParasitesGood.ImageNumber)
AND (MyTable_Per_ParasitesGood.ParasitesGood_Number_Object_Number = MyTable_Per_ParasitesGood_Classes.ParasitesGood_Number_Object_Number)
AND MyTable_Per_ParasitesGood_Classes.class='positive'
ORDER BY Image_Metadata_Plate, Image_Metadata_Well, ABS(Image_Metadata_Site), ABS(MyTable_Per_Image.ImageNumber) 

Though you’d have to modify this for your table and column names.

Amazing. Thank you David!

This may be helpful to others:

Another option to achieve this is within Table Viewer. Load from the database with the “Objects” selected. Then save this file as CSV1. Then do the same but this time instead of “Objects” select “Classifier”. Save this file as CSV2. Then copy the files from CSV2 into CSV1 and use conditional formatting in Excel to color-code the words “positive” or “negative”. Then use custom sorting to separate the two populations for scrutiny.

Amazing Software!! Love It!

-Michael
OSU CHS

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