Webinar

Image Processing in KNIME

Martin Horn and Christian Dietz
University of Konstanz

Copyright © 2014 by KNIME.com AG. All rights reserved.

 What’s KNIME?

Copyright © 2014 by KNIME.com AG. All rights reserved.

 What’s KNIME?
• Data integration, processing, analysis and exploration platform
• User-friendly, open-source and easy updatable
• Software integration platform
• Highly modular, easily extendible
• Workflow based & Cluster execution
• Current Version: KNIME 2.9.2

www.knime.org

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 What’s KNIME?

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 Why Image Processing in KNIME?

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 Image Processing Tools
Development Processing UI IO/Storage

ImgLib2 ImageJ OMERO

SciJava ImageJ2 SCIFIO
OpenCV Fiji BioFormats
MatLab CellProfiler …
NumPy Ilastik
VTK CellCognition
VIGRA Icy
… Photoshop
…

=
Huge variety of image processing tools
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 KNIME as Integration Platform

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 KNIME just for Integration?
• Data Caching (High-Throughput!!)
• Fast Prototyping
• Automation
• Interactive Data Exploration
• Machine Learning
• Bridging Domains
• …

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 KNIME Image Processing Universe
Tess4J

SUISE ImageJ
KNIME Image
Processing
1.1.2
KNIME Image
Processing
1.1.2
OMERO Trackmate

ImageJ3D
VTK
Viewer

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 KNIME Image Processing Universe
Tess4J

SUISE ImageJ
KNIME Image
Processing
1.1.2
KNIME Image
Processing
1.1.2
OMERO Trackmate

ImageJ3D
VTK
Viewer

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 KNIME Image Processing Universe
Tess4J
ImageJ 3D Viewer
SUISE ImageJ Visualization of 3d to 5d images
http://3dviewer.neurofly.de
KNIME Image
Processing
1.1.2
OMERO Trackmate

ImageJ3D
VTK
Viewer

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 KNIME Image Processing Universe
Tess4J
Trackmate
SUISE ImageJ Allows tracking of objects in KNIME
http://fiji.sc/TrackMate
KNIME Image
Processing
1.1.2
Future Work
OMERO Trackmate
Better visualization of tracks
Calculation of tracking features

ImageJ3D
VTK
Viewer

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 KNIME Image Processing Universe
Tess4J
Tess4J
SUISE ImageJ Optical Character Recognition
Java Wrapper of Tesseract OCR
KNIME Image
Processing
1.1.2
Future Work
OMERO Trackmate
MAC support

ImageJ3D
VTK
Viewer

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 KNIME Image Processing Universe
Tess4J
Supervised Image Segmentation
SUISE ImageJ
(experimental)

KNIME Image
Processing
1.1.2
OMERO Trackmate

ImageJ3D
VTK
Viewer

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 KNIME Image Processing Universe
Tess4J
OMERO
SUISE ImageJ Tools for storing visualizing, managing
and annotating microscopic images
and metadata
KNIME Image
Processing
1.1.2
OMERO Trackmate

ImageJ3D
VTK
Viewer

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 KNIME Update Mechanism
Install new Plugins/Updates

KNIME
Update-
Site
KNIME
Provide Updates/Plugins

• File -> “Update KNIME “

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 KNIME Update Mechanism
KNIME.com
KNIME
Update-
Site KNIME
… Labs
Update-
Anyone how likes Site
to contribute!
Your
Update- KNIME
Site

Trusted
Stable Update-
Site
Update-
Site
Community Contributions
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 Organisation of Plugins

Imaging Community Contributions

Trusted Stable
• KNIME Image Processing • ImageJ Integration
• OMERO Integration • Tess4J
• Supervised Segmenation
• VTK 3D
• ImageJ 3D

Trusted Update-Site Stable Update-Site

Nightly Builds

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 Install KNIME Image Processing (Trusted)
• Click on File -> “Install KNIME Extensions”
• Select KNIME Community Contributions – Imaging
• Follow the instructions

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 Install KNIME Image Processing (Stable)
• Help -> „Install New Software“
• Click on „Available Software Sites“

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 Install KNIME Image Processing (Stable)
• Activate “Community-
Contributions“ Update-Site
• Confirm with “OK“

• Now: Same as for Trusted!

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 Website/Contact
• Update Site
• Installation Details, News, Wiki, GitHub
• Forum
• Contact Information
• Example Workflows/Tutorials

http://tech.knime.org/community/image-processing
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 Live-Demo

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 Live-Demo Agenda
• The Image Data Type (ImgPlus-Cell)
• Example: High-Content-Screening
• Group images and Image Calculator
• Global Thresholding
• Segmentation (CCA and Region Growing)
• Segment features
• Filter segmentations
• Explore segmentation results

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 Example: High-Content-Screening

Positive Negative

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 Example: High-Content-Screening

http://www.broadinstitute.org/bbbc/BBBC013/

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 ImageJ Integration

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 ImageJ / FIJI
• Very popular, highly interactive image processing tool
• Many available plugins
• Fiji: Extension of ImageJ1 with plugin-update
mechanism and plugins

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 ImageJ2
• Next-generation version of ImageJ
• Complete re-design of ImageJ while maintaining backwards
compatibility
• Based on ImgLib2

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 ImageJ2 in KNIME
• Automatic node generation
• Add own ImageJ2 Plugins via installer
• Currently in BETA (as ImageJ2 is BETA)

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 Work in Progress
KNIME in ImageJ2
• Run Workflows as ImageJ2 Plugins (headless)
• Record Workflows in ImageJ2

ImageJ2 in KNIME
• Enable use of IJ2-Update Site in KNIME

ImageJ-Ops
• Common framework for image processing algorithms
• Started two weeks ago: Hackathon in Konstanz with ImageJ2 Team

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 Goal: Full Bidirectional Integration

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 Outlook

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 Future Work
KNIME Image Processing 1.2.0
• New Image Writer Node
• New Image Segment Feature Node
• Better support of color tables
• Support for huge images (>memory capacity)

Collaborations with IJ2/FIJI/ImgLib2/…

• Ops, ROIs, ….

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 Upcoming Events
Next Webinars:
• Empowering your Team with KNIME Server, April 30
Next Meetup: Boston, May 14
Next Hands-on Trainings:
• Seattle: March 19
• Austin: March 25
Next User Training, Zurich: KNIME User Training, April 7-9

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 Thank you…
education@knime.com

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