Reverse the Odds

Scripts to analyse histopathological classifications from the Cancer Research UK Citizen Science game Reverse the Odds. At current stage not very useful unless you have direct access to the data, which is not publicly available for now.

For internal use, the following files are required but not available on github:

• classifications and subjects collections imported into MongoDB

Steps to analyse the data

• Import classifications and subjects into mongoDB, and set the correct db name in rto_mongodb_utils.py
• Run rto_mongodb_utils with all functions uncommented to preprocess/clean the data (if errors, probably because stain names are inconsistent; track down and add correction to rto_mongodb_utils.py)
• Run user_aggregation.py for each stain type, once with bootstrap turned off, once turned on (and aggregate = 'ignoring_segments'). This will fill up the 'results' database in mongoDB with collections 'bootstraps' and 'cores')
• Run patient_level.py's pll.combine_cores_per_patient() to generate a 'patients' collection with each stain aggregated for each patient. This also creates excel files for easy sharing with research groups

Then you can plot results with core_level_plots.py or patient_level.py

Copyright / Licence

Copyright 2016/2017 Cancer Research UK

Source Code License: The GNU Affero General Public License, either version 3 of the License or (at your option) any later version. (See agpl.txt file)

The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software.

Documentation is under a Creative Commons Attribution Noncommercial License version 3.