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CellProfiler as a Python package
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In addition to running CellProfiler’s graphical-or-command-line interface, CellProfiler is usable from any Python environment (e.g. a Python interpreter, Jupyter Notebook, or a Python package).
A public (and stable) interface is forthcoming — feedback is encouraged.
Open a pipeline
import cellprofiler.pipeline pipeline = cellprofiler.pipeline.Pipeline() pipeline.load("example.cppipe")
Run a pipeline
measurements = pipeline.run()