KNIME Image Processing

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KNIME Image Processing

KNIME is the leading open platform for data-driven innovation. It also has an ImageJ integration as part of the KNIME Image Processing Plugin (KNIP) developed at the University of Konstanz.

KNIP allows you to model image processing operations as KNIME Workflow and inspect the results after every step.


Integrate image processing into your data analysis and take all your favorite tools with you:

  • ImageJ
  • R Scripting
  • Python Scripting
  • Feature extraction
  • Machine Learning (native and Weka)
  • Read and write to many different data sources:
    • Databases
    • XML / JSON
    • CSV
  • thousands of other nodes and possibilities

KNIP is supported on the KNIME forums and GitHub—you can ask questions and report bugs there.

Getting Started

  1. Download KNIME
  2. Follow the instructions on the getting started page


You can find example of what you can do with KNIP on our example page.

Quantitative analysis of an image
Identify nuclei and spots in imageJ
How do I measure differences in distance between different pictures?
Segmentation - counting cells in 3D
How to get the coordinate of a sphere in a series of high speed photographs?
Eye Tracking on IR image
Split large image into smaller images for batch processing
Cell counting analysis
Creating one Histogram of multiple ROIs
Quantify fluorescence within a cell within a stack
Sum region of binary image by column
BoneJ Particle Analyzer Macro commands
3D segmentation over time
Distance between particles
Batch Processing without opening image
Run a plugin on multiple images to get an output image and a table
Automatic diameter statistics for rising bubbles
Protozoa recognition : Looking for help
Measuriing Aorta wall thickness
Measuriing Aorta wall thickness
Dots Analysis project for industrial use for a total begginer
Alive vs Dead Specimen Analysis
Calculation of porosity on 2D image with bad threshold
Image Analysis for bacteriophage Plaques
Findmaxima fails
Bug/issue opening mha files
How can I measure ALL the shortest distances between all ROIs in an image?
Counting dots and distance in ImageJ?
Extracting spot intensity values from TrackMate files
Analyse the directionality of nanofibers
Calculation of the length of a moving intestine in a movie
Macro for batch processing image conversion
Macro for bulk processing/cropping of images
Batch measuring artefacts
Automatically Detecting transcription sites in image stacks and measuring
DICOM info AND measurements for multiple ROIs for a CT stack
Pattern analysis of nets used in fish farming
Finding ellipses with incomplete boundaries
Select ROIs in the ROI manager according to the measured data
Random ROI generator
3D object counter - Is there a way to make it use more than one CPU core?
Batch & Macro: Read out Values from (txt) XML File
Analysis of binarized images to discriminate elements expressing other elements
Problem in area measurement after threshold with Analyze Particles
Bio-Formats accessors with ImgPlus metadata
Creating object class with rois from multiple channels
DNA Quantification through Fluorescence Intensity in Neurons/Double Staining IHC
How Can I Find Size, Angle and Vector(line) Length Automatically or using single button click or macro :)
Re: converting XML file to ImageJ format
3D project in other modes (eg. StDev)?