Community Contributions

User login

Image Processing and Analysis in KNIME

Fri, 12/03/2010 - 13:09 — knime_admin

Used and integrated libraries

Omero^(1,2)

(1) 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.

(2) The OMERO integration is unfortunately only prototypic so far and we are planing to make a stable integration available as soon as possible. More details regarding the OMERO integration can be found here.

Overview

These image processing nodes add new image types to KNIME and the corresponding nodes to read more than 100 different kinds of images (thanks to the Bio-Formats API), to apply well known methods for the preprocessing and to perform image segmentation. It replaces the outdated Image Processing plugin that was previously hosted on KNIME Labs. Most of the included 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.

In addition several nodes are included 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.

The Image Processing Plugin for KNIME currently provides ca. 70 nodes for (pre)-processing, filtering, segmentation, feature extraction, various views, ... .

>> How to install KNIME Image Processing? <<

FAQ

News

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.

Example workflows

To run the workflows please install the Math-Formula plugin to also see the analysis. This is not needed, but a error will be thrown if it is not installed. the workflows run anyway!

High-Content Screening
Segments, classifies and analyses cells (images included)
details, biological background and image set are available at Click here
Count Chromosomes
Counting the number of chromosomes for each nuclei (data included). Requires installation of ImageJ integration.
Larva-Tracking
Simple larva tracking and extracting the (x,y) position for each time-frame. Data can be downloaded here.
Measure Intensity
Simple workflow where some statistics on the intensity of cells are calculated.
ImageJ Example Workflow
Simple ImageJ2 example workflow making use of the "Add noise plugin".

Contact

If you have suggestions, problems, etc. don't hesitate to contact us! We are glad to help you.

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

Main menu

Search