cytomining / pycytominer

Python package for processing image-based profiling data
https://pycytominer.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Add single cell normalization options #100

Open gwaybio opened 4 years ago

gwaybio commented 4 years ago

The most common entrypoint to pycytominer is in the form of sqlite files. These files contain tables for each compartment, which themselves contain single cell morphology measurements.

Increasingly often we need to use normalized single cell profiles. We need to consider how to modify the sqlite files in a way that makes the single cell data easier to compute on.

It is possible that this issue coexists somewhere between pycytominer and cytominer-database.

gwaybio commented 4 years ago

My strategy here will be to abstract out the AggregateProfiles() class into a new cytominer singlecell.py method.

gwaybio commented 4 years ago

I ended up extracting AggregateProfiles from aggregate.py into a new script cyto_utils/cells.py.

@hillsbury noted that the single cell normalization procedure for aggregate profiles is not likely to work the same as for bulk profiles.

gwaybio commented 3 years ago

Normalization options for single cell data still need to be explored. The single cell module is now available after merging #111