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cytomining / cytominer-database

[DEPRECATED] A package for storing morphological profiling data.
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Cytominer learning #125

Open ManonFepi opened 4 years ago

ManonFepi commented 4 years ago

Hi! I am newly working on high content screening and I would like to use cytominer to analyse my data. But I have some issues following your pipeline. I have create my database with information about cells, nucleus and cytoplasm like your "fixture_htqc.sqlite" but from this point, I don't understand how you get your "fixture_intensities_shapes.sqlite". Did you managed it with python and sqlite3? I someone could help me and give me some advice to better understand what you've done, it will be so nice!

Thanks in advance, Have a nice day, Manon

gwaybio commented 3 years ago

Hi @ManonFepi - I just saw this issue, sorry for the delay. Were you able to solve the issue? If not and you are still interested, we use either sqlite3 or sqlalchemy to interact with sqilte files in python.

An example of sqlite3 is here: https://github.com/broadinstitute/profiling-resistance-mechanisms/blob/d76a8a4b1d41c071653e48fb01be73dab32ddc52/4.single-cell/scripts/nbconverted/0.train-test-split.py#L103

An example of sqlalchemy is here: https://github.com/cytomining/pycytominer/blob/9f85ca450204a459f1afcb23a3c634ae5eb325c4/pycytominer/aggregate.py#L79

hope this helps!