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AAEC 2015 KNIME for Open-Source BioImage Analysis - A Tutorial

KNIME for Open-Source BioImage Analysis - A Tutorial

The next steps will help you to install KNIME and KNIME Image Processing in order to reproduce the Phenotype Classification workflow discussed in KNIME for Open-Source BioImage Analysis - A Tutorial, Advances Anatomy Embryology and Cell Biology - Focus on Bio-image Informatics.

1. Installation of KNIME and KNIME Image Processing

  • Download and Install KNIME 3.0.0: https://www.knime.org/downloads/overview
  • Install KNIME Image Processing 1.4.0. The  KNIME Analytics Platform as well as all other KNIME products are linked automatically to the KNIME Update Site through the File menu via the "Install KNIME Extensions" command.
  • Install the KNIME ImageJ2 Integration as described here.

2. Downloading and importing the Workflow

  • Download the workflow here.
  • Import the workflow into KNIME (File -> Import KNIME Workflow ... -> Select Archive File)

Notes:

  • We suggest that you adapt the local memory settings according to your system to at least -Xmx2048m.
  • The workflow already contains the image data, therefore we don't use the List Folder node to list the files we want to load. We used the Image Reader Dialog to select the images and load them. The Phenotype Classification workflow is ready to be executed, after you have downloaded it.
  • If you use the workflow with a  KNIP version > 1.4.x, some nodes may be deprecated (see node description for deprecation reasons). The workflow will still work as expected and produce the correct results, however there may exist newer versions of some nodes used in the workflow.

3. Further information