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Cell Clump Splitter (Deprecated)

StreamableKNIME Image Types and Nodes version 1.8.3.202012050717 by University of Konstanz

Splits cell clumps according to the implemented paper (1)

(1) Chanho Jung, Changick Kim, Seoung Wan Chae and Sukjoong Oh, unsupervised segmentation of overlapped cells using bayesian classification, IEEE Transactions on, 2010 (http://cilabs.kaist.ac.kr/People/Paper/05518403.pdf)

Options

Minimum Value of a Local Maxima
Ignore local maxima values that lie below this value.
Ignore Percentage
Ignore local maxima values below the percentage of the average value of local maximas of the clumped cell. Value is between 0 and 1.
Neighboorhood
Neighborhood definition. Ignore local maxima whice have a local maxima in their radius.
  • EIGHT: check Neighboors within radius 1
  • SIXTEEN: check Neighboors within radius 2.
  • THIRTYTWO: check Neighboors within radius 3.
Maximum Number of Iterations
Number of iterations of the performed EM algorithm.

Column Selection

Column Creation Mode

Mode how to handle the selected column. The processed column can be added to a new table, appended to the end of the table, or the old column can be replaced by the new result

Column Suffix
A suffix appended to the column name. If "Append" is not selected, it can be left empty.
Column Selection
Selection of the columns to be processed.

Input Ports

Icon
Labeling

Output Ports

Icon
Labeling with Splitted Objects

Views

Image Viewer
Another, possibly interactive, view on table cells. Displays the selected cells with their associated viewer if it exists. Available views are:
- XML
-- XML tree
- Histogram Viewer
-- This viewer shows the histogram of the currently selected image.
- Missing Value Viewer
-- An empty viewer that is shown when the input cell has no value to display.
- Combined View
-- A viewer shown when the user selects an interval of rows and columns in the viewer. This viewer combines all images and labelings in the selected interval to one image by rendering them next to each other. Alternatively, the images and labelings can be layed over each other.
- Image Viewer
-- This viewer renders the selected image-cell.
- Labeling View
-- View on a labeling/segmentation
- BigDataViewer
-- A viewer shown when the user selects an interval of rows and columns in the viewer. This viewer combines all images and labelings in the selected interval to one image by rendering them next to each other. Alternatively, the images and labelings can be layed over each other.

Installation

To use this node in KNIME, install KNIME Image Processing from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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