KNIME Image Processing
Nycomed Chair for Bioinformatics and Information Mining Department of Computer and Information Science Konstanz University, Germany Why Image Processing with KNIME?
KNIME UGM 2013 2 The “Zoo” of Image Processing Tools
Development Processing UI Handling
ImgLib2 ImageJ OMERO OpenCV ImageJ2 BioFormats MatLab Fiji … NumPy CellProfiler VTK Ilastik VIGRA CellCognition … Icy Photoshop … = Single, individual, case specific, incompatible solutions
KNIME UGM 2013 3 The “Zoo” of Image Processing Tools
Development Processing UI Handling
ImgLib2 ImageJ OMERO OpenCV ImageJ2 BioFormats MatLab Fiji … NumPy CellProfiler VTK Ilastik VIGRA CellCognition … Icy Photoshop …
→ Integration!
KNIME UGM 2013 4 KNIME as integration platform
KNIME UGM 2013 5 Integration: What and How?
KNIME UGM 2013 6 Integration
ImgLib2 • Developed at MPI-CBG Dresden • Generic framework for data (image) processing algoritms and data-structures • Generic design of algorithms for n-dimensional images and labelings • http://fiji.sc/wiki/index.php/ImgLib2
→ KNIME: used as image representation (within the data cells); basis for algorithms
KNIME UGM 2013 7 Integration
ImageJ/Fiji • Popular, highly interactive image processing tool • Huge base of available plugins • Fiji: Extension of ImageJ1 with plugin-update mechanism and plugins • http://rsb.info.nih.gov/ij/ & http://fiji.sc/
→ KNIME: ImageJ Macro Node
KNIME UGM 2013 8 Integration
ImageJ2 • Next-generation version of ImageJ • Complete re-design of ImageJ while maintaining backwards compatibility • Based on ImgLib2 • http://developer.imagej.net/
→ KNIME: Tight integration – Automatic node generation from ImageJ2-plugins
KNIME UGM 2013 9 Integration
BioFormats • Library for reading and writing > 120 image file formats • OME-XML standard • http://loci.wisc.edu/software/bio-formats
→ KNIME: Image Reader and Writer
KNIME UGM 2013 10 Integration
OME / OMERO • Tools for storing (OMERO database), visualizing, managing and annotating microscopic images and metadata • http://www.openmicroscopy.org/
→ KNIME: Experimental OMERO Reader
KNIME UGM 2013 11 The KNIME Image Processing Extension – An Example
KNIME UGM 2013 12 Some Nodes Input/Output Image Proc. Segmentation
Features
Views
KNIME UGM 2013 13 Example: High-Content Screening
KNIME UGM 2013 14 Example: High-Content Screening
positive negative
KNIME UGM 2013 15 Example: High-Content Screening
KNIME UGM 2013 16 Example: High-Content Screening
KNIME UGM 2013 17 Example: High-Content Screening
KNIME UGM 2013 18 Example: High-Content Screening
KNIME UGM 2013 19 Example: High-Content Screening
KNIME UGM 2013 20 Example: High-Content Screening
KNIME UGM 2013 21 Example: High-Content Screening
KNIME UGM 2013 22 … KNIME UGM 2013 23 Resources
• Workshop tomorrow! • Homepage: http://tech.knime.org/community/image- processing • Forum: http://tech.knime.org/forum/knime-image- processing • Contact: [email protected] [email protected] [email protected]
KNIME UGM 2013 24 Thank you…
KNIME UGM 2013 25