Classifier tool, multiple images per set, independent classes, and thumbnails


#1

Hello esteemed CellProfiler Team!

I have only recently started working with CPA 2.0 (let me thank you, I wish I had done so earlier), and obviously I have questions :wink:

  1. Let’s assume my CP pipeline (and exported SQLite db) contains multiple measurements and images per set (e.g measurements of DNA, proliferation marker, auxiliary nuclear marker). Is it possible to define settings that govern which images or measurements may (or more importantly, may NOT) be used for finding classifier rules? Sometimes I find the “Objectnumber” listed among the rules, at other times I wish to simply ignore a measurement or image (and compare it to my preliminary classification later). Removing these via “Edit Rules” would need to be repeated after every training cycle.

  2. Is there a possibility (or any workaround) to create two independent classifications per database? (e.g. classify cells according to marker A, then create a second classification table and classify them via marker B (and later confront the two independent classifications?). Currently, I process two (or more) markers in separate projects and databases, then classify cells and export .csv tables seperately, finally joining them in Excel for comparison (and after getting used to CPA, I’d really like to avoid spreadsheets =D). Can I link two (or more) per_object classification tables from seperate databases? (Or alternatively, do you think I could load my jury-rigged spreadsheet into the database and use it in CPA?)

The columns of the (compound) classification tables I would like to produce might resemble:

Image_number, Object_number, Marker_A_class_number, Marker_A_class_name, Marker B_class_number, Marker_B_class_name (etc etc).

  1. Thumbnails (edit - found solution)

I appreciate your tools and your help! Also I can’t help but think there is a simpler method I failed to recognise…


#2

Hi @Fabba123,

  1. Try out the new CellProfiler Analyst 2.2.1. (Look into installation). We added a new normalization tool, which allows you to generate a new database where you can throw away some columns. After creating a new database, just change your object_table in your properies file to the new generated database name and restart CPA with the new properties file.

  2. With CellProfiler Analyst 2.2.1 it is now possible to open multiple classifier (we are also supporting new classifiers). But currently we don’t provide any option to link classification results together. Maybe in the future!

Hope that helps.

David


#3

Edit your properties file and search for a setting with “ignore”. You can specify columns to ignore.


#4

Looking forward to trying the new version! Thanks!