HistogramOfDeconvolutedImagesWithOriginal

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This workflow converts the input images selected in the Image reader to histograms in different output formats.

It uses the colour deconvolution plugin: https://github.com/sunsear/colour_deconvolution_IJ2 to do the deconvolution.
The released version can be found on https://search.maven.org/artifact/com.github.sunsear/Color_Deconvolution_IJ2.
This workflow uses the 1.0.0 version.

For every input image the output is one colum with the histogram data for every deconvoluted image (3) and one column with the histogram of the original. The original is first converted to grayscale.

The remove high values is used to remove the histogram peak for the white background values
There are 3 options
0. All values >10 times than the mean of the column are removed
1. no values are removed
2. all values >100.000 are removed
Selection of the type can be done in the configuration of the "Remove high values" component.
The specific defaults can be found in the Math Formulas and can also be changed there.
There is also an option for writing every created image to file in the "Write every image to an image file" box.

Image reader:
In the image reader you can select the images for the deconvolution. Because the path is user specific and can not be made relative on first use you have to clear all selected images and selected the images on your system. After that it should all work.
You have to select the proper image reader directory yourself before it will work.

The report box creates an report to excel with in every cell one image.
To write all images to an excel document:

1. Execute the "Data to Report" node
2. Click on the report icon from the toolbar to open the report
3. Click in the reportwindow on the view report button in the toolbar. The report is opened in the browser.
4. Click on the export button in the report view and select XLSX as export type.
The xlsx file is downloaded in the browser.


Installation:
To use this workflow in KNIME there should be installed:
KNIME 4.1 or higher
extensions:
KNIME Image Processing
KNIME JavaScript Views (Labs)
KNIME Image Processing - ImageJ Integration (Beta)
See also: https://www.knime.com/wiki/install-knime-image-processing

The color deconvolution plugin:
https://github.com/sunsear/colour_deconvolution_IJ2
or
https://search.maven.org/artifact/com.github.sunsear/Color_Deconvolution_IJ2
to do the deconvolution.

For installation of the color deconvolution plugin see:
https://github.com/sunsear/colour_deconvolution_IJ2/blob/master/docs/INSTALL_KNIME.md

Nodes

• Column Filter10 ×
• Column Rename8 ×
• Column Rename (Regex)8 ×
• Component Input6 ×
• Component Output6 ×
• String Manipulation6 ×
• Split Collection Column5 ×
• Java Snippet4 ×
• String To Number4 ×
• Transpose4 ×
• Column Splitter3 ×
• Concatenate3 ×
• Double Configuration3 ×
• Joiner3 ×
• Column List Loop Start2 ×
• Excel Writer2 ×
• Loop End (Column Append)2 ×
• Math Formula2 ×
• RowID2 ×
• Variable to Table Column2 ×
• CASE Switch End1 ×
• CASE Switch Start1 ×
• CSV Writer1 ×
• ColorDeconvolutionIJ2FromValues1 ×
• Column Resorter1 ×
• Column Selection Configuration1 ×
• Data Explorer (JavaScript)1 ×
• Data to Report (BIRT)1 ×
• Image Calculator1 ×
• Image Reader1 ×
• Image Writer1 ×
• Line Plot (JavaScript)1 ×
• Splitter (uncropped)1 ×
• String Input1 ×
• String Manipulation (Variable)1 ×
• Table Row to Variable Loop Start1 ×
• Variable Loop End1 ×

Extensions

• FeatureKNIME Base nodes
• FeatureKNIME Excel Support
• FeatureKNIME Image Processing
• FeatureKNIME JavaScript Views
• FeatureKNIME JavaScript Views (Labs)
• Show all 9 modules

Links

• Deconvolution plugin

  github.com/sunsear/colour_deconvolution_IJ2
• Installation guide for the deconvolution plugin

  github.com/sunsear/colour_deconvolution_IJ2/blob/master/docs/INSTALL_KNIME.md
• Installation KNIME image processing

  www.knime.com/wiki/install-knime-image-processing
• Release version of the deconvolution plugin

  search.maven.org/artifact/com.github.sunsear/Color_Deconvolution_IJ2