The KNIME Image Processing Extension allows you to read in more than 140 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.
Here are the available KNIME Image Processing extensions:
- ImageJ
- OMERO
- Supervised Image Segmentation
- Tesseract (OCR)
- Ilastik
- CellProfiler
- ClearVolume
- Image Processing Python Extensions
Overview
- Getting Started Guide
- KNIME Image Processing Forum
- KNIME FAQ
- KNIME Image Processing on GitHub
- Contact
Getting Started
Installation
Internal Resources
- Cite us: KNIME for Open-Source BioImage Analysis - A Tutorial (Paper, Preprint, Website)
- KNIME Image Processing (Webinar on YouTube)
- Example Workflows and Tutorials
External Resources
- Big Imaging Course with KNIME (Kevin Mader, ETH Zuerich)
- VT Science Week Course with KNIME (Kevin Mader, ETH Zuerich)
- Biodesign Imaging Workshop (Kevin Mader, ETH Zuerich)
- Keynote on KNIME Image Processing (Florian Jug MPI Dresden @ ImageJ Conference UW-Madison 2015)
Example Workflows
You can browse the KNIME Image Processing-related example workflows on KNIME Hub. There, you will find example applications and tutorials including information about the content of the workflow and how to get the workflow running.
Used and integrated libraries
| BioFormats | SCIFIO | ImageJ | ImageJ2 | OMERO | SciJava |
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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, challenges, etc. please post in the Image Processing category in our forum! We are glad to help you there.
License
The KNIME Image Processing nodes are released under GPLv3.
