KNIME Image Processing - CellProfiler Integration

Collaborative project of CellProfiler (Broad Institute) and KNIME Image Processing (University of Konstanz).


The KNIME Image Processing - CellProfiler Integration allows to run CellProfiler Pipelines within KNIME. All pipelines which take images as input and output a feature-table in CellProfiler are supported.


Please Note: You have to install the latest 'bleeding-edge'  nightly-version of CellProfiler in order to use the KNIME Image Processing - CellProfiler Integration. You can download the latest 'bleeding-edge' version of CellProfiler here.

Currently, CellProfiler is only available with the NightlyBuild of KNIME Image Processing. Therefore you have to conduct the following steps to install the KNIME Image Processing - CellProfiler Integration:

1. Download and install KNIME from /downloads/overview (without extensions, just KNIME). If you need help see /learning-hub

2. Install the KNIME Image Processing - CellProfiler Integration from the Stable Community Contributions Update-Site (see /wiki/install-knime-image-processing 2.2)

3. In KNIME: Go to File -> Preferences -> KNIME -> CellProfiler and enter the directory of your CellProfiler integration.

Please make sure that you have enough memory available. See: /faq#q4_2

Example Workflows

We moved all our Example Workflows to the KNIME Example Server: /example-workflows. In the category 099_Community/ you will find example applications & tutorials for all our integrations including information about the content of the workflow and how to get the workflow running.


Links and Ressources


  • Lee Kamentsky (Broad Institute): leek (at) broadinstitute.org
  • Patrick WInter (University of Konstanz): patrick.winter (at) uni-konstanz.de
  • Christian Dietz (University of Konstanz): christian.dietz (at) uni-konstanz.de



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