CellProfiler as a Python package

Allen Goodman edited this page Sep 13, 2016 · 11 revisions

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.

Quick start

CellProfiler pipelines

Open a pipeline

import cellprofiler.pipeline

pipeline = cellprofiler.pipeline.Pipeline()

pipeline.load("example.cppipe")

Run a pipeline

measurements = pipeline.run()