KNIME Image Processing (trusted extension)


Overview

The KNIME Image Processing Plugin allows you to read in more than 120 different kinds of images (thanks to the Bio-Formats API) and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME. In general these nodes operate on multi-dimensional image data (e.g. videos, 3D images, multi-channel images or even a combination of them), which is made possible by the internally used ImgLib2-API.

Several nodes are available to calculate image features (e.g. zernike-, texture- or histogram features) for segmented images (e.g. a single cell). These feature vectors can then be used to apply machine learning methods in order to train and apply a classifier.

Currently the Image Processing Plugin for KNIME provides ca. 100 nodes for (pre)-processing, filtering, segmentation, feature extraction, various views (2D, 3D), etc. and integrations for various other image processing tools are available (see used and integrated libraries)

Future directions include a full, bidirectional integration of ImageJ2. Such an integration allow the users to use directly use/update ImageJ2 Plugins inside KNIME as well as recording and running KNIME Workflows in ImageJ2. Please see ImageJ2 Integration (BETA) for more information.

For the first steps please consider the KNIME Image Processing User Manual (incomplete draft!).

Important Links

 

Example Workflows

Some worklfows will optionally need the Math-Formula node for the further analysis which can be installed via the KNIME-update site. The example workflows have been created with the latest version of KNIME (currently KNIME 2.8).

Applications

Reproduced examples provided by CellProfiler

  • High-Content Screening
    Segments, classifies and analyses cells (images included)
    details, biological background and image set are available at Click here
  • Yeast Colonies (Since KNIME - Image Processing 1.1.0)
    Segments and classifies yeast cells on a plate.

ImageJ2 Examples

Generic Examples

  • Don't Save Node (Since KNIME - Image Processing 1.2.0)
    Workflow demonstrating the usage of the Don't Save nodes.
  • Slice Iterator Loop (Since KNIME - Image Processing 1.2.0)
    Workflow demonstrating the usage of the Slice Iterator Loop nodes.
  • 3D Segmentation (Since KNIME - Image Processing 1.2.0)
    Workflow demonstrating one possibility to segment objects in 3D images.
  • Cell Clump Splitter 2D (Since KNIME - Image Processing 1.2.0)
    Workflow demonstrating how to split cell clumps in 2D.

Tutorials

 

News

07/10/2014 KNIME Image Processing 1.2.0 is now available. Please see http://tech.knime.org/forum/knime-image-processing/knime-image-processin... for details.
04/05/2014 Announcement of ImageJ-Ops:  http://developer.imagej.net/2014/04/04/announcing-imagej-ops
02/11/2014 Another very small bugfix-release 1.1.2.
01/13/2014 The bugfix-release 1.1.1 is now available. Issues resolved with this version are listed here.
12/06/2013 KNIME Image Processing 1.1.0 has been released with KNIME 2.9.0. Besides several fixed bugs and improvements, a few new nodes have been added (see changelog). Moreover, the list of available tutoriales and example workflows has been extended.

08/28/2013

KNIME Tesseract (OCR) Integration Beta version released. The integrations enables users to read in images containing text and convert them to real characters, which then can e.g. can be processed using the KNIME Text Processing Extension.

For more details click here.

07/24/2013

KNIME Image Processing 1.0.4 (KNIME 2.7) and KNIME Image Processing 1.0.5 (KNIME 2.8) released. Basically we fixed a lot of bugs but we also provide new nodes or enhancements of existing nodes, like Labeling to PNG Images, Labeling to RGB Img, Labeling Filter and Local Thresholder. Additionally we improved our MemoryManagement (available with KNIP 1.0.5) and the support of ColorTables.

See the change log for further details.

If you face any problems, feel free to contact us via the forum or email.

12/10/2012

KNIME Image Processing 1.0.3 released. We fixed several bugs and added new features to existing nodes. For instance we moved the functionality of the Image Group By Node to the standard GroupBy Node of KNIME. We also fixed several bugs in the VTK integration, the ImageJ integrations and the OMERO integration.

See the change log for further details.

Remark: If you want to use KNIME Image Processing 1.0.3, you have to update to KNIME 2.7.

09/13/2012

KNIME Image Processing 1.0.2 released. Several bugs were fixed and a new caching system for images and labelings was introduced. 

Please see changelog for details.

08/24/2012

KNIME Image Processing 1.0.1 released. Several bugs were fixed and especially some major memory leaks were closed!

Please see changelog for details.

07/29/2012

Release of a first mature version of the KNIME Image Processing Extension 1.0.0. Within releases of this major version number (i.e. 1.*.*) we try hard to be backwards compatible whenever possible, e.g. such that all workflows created once (with a 1.*.* release) can be restored with the newest plugin version.

Used and integrated libraries

ImgLib2

BioFormats

SCIFIO

SCIFIO

ImageJ

ImageJ2

OMERO

OME logo

ImageJ and OMERO integrations are organised in extra plugins (also available via the community contributions update site). See 'ImageJ' and 'OMERO' for more details of the respective integration.

 

Contact

If you have suggestions, problems, etc. don't hesitate to write in the our forum or contact us! We are glad to help you.

Christian Dietz Nycomed Chair for Bioinformatics and Information Mining, University of Konstanz
   
Martin Horn Nycomed Chair for Bioinformatics and Information Mining and Research School Chemical Biology, University of Konstanz