Global Thresholder

A threshold algorithms automatically (or manually) determines a threshold to distinguish between foreground and background of an image. After the threshold has been computed or manually chosen selected, the algorithm marks any pixel with an intensity value greater than this threshold with "1" and any pixel with intensity lower than the threshold as "0". The result is a binary image which subsequently can be processed with the Connected Component Analysis Node to extract a labeling with separated segments. For details see: "Survey over image thresholding techniques and quantitative performance evaluation" (Sezgin04)

Options

Manual Threshold: The threshold value used if MANUAL is used as threshold value.
Thresholding Method: The thresholding method to determine the threshold.
Dimension Selection: This component allows the selection of dimensions of interest. If an algorithm cannot, as it only supports fewer dimensions than the number of dimensions of the image, or shouldnot, as one wants to run the algorithm only on subsets of the image, be applied on the complete image, the dimension selection can be used to define the plane/cube/hypercube on which the algorithm is applied. Example 1 with three dimensional Image (X,Y,Time): An algorithm cannot be applied to the complete image, as it only supports two dimensional images. If you select e.g. X,Y then the algorithm will be applied to all X,Y planes individually. Example 2 with three dimensional Image (X,Y,Time): The algorithm can be applied in two, three or even more dimensions. Select the dimensions to define your plane/cube/hypercube on which the algorithm will be applied.

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.

ROI Options

Labeling Column

If you choose a column with a labeling here, the node will only operate on the Regions of Interests (ROIs) which are defined by the incoming labeling!

Filling Mode

The FillingMode determines how all values, which lie outside your defined region of interest, will be set. This option is only needed if you choose a labeling column, such that the node operates on ROIs instead of the entire image. There are currently four FillingModes:

Value of Source: In this mode, pixels outside of the ROIs remain unchanged.
Minimum of Result Type: Here, values outside of the ROI are set to the smallest legal value of the output image type.
Maximum of Result Type: All values outside of the ROI are set to the largest posible value of the output image type.
No Filling: No action is taken after initializing the target image, thus all pixels outside the ROIs remain zero.

Input Ports

: Images

Output Ports

: Thresholded binary images.

Popular Predecessors

CLAHE6 %
~~Joiner~~4 %
~~Row Filter (deprecated)~~4 %
Min Filter3 %
Splitter3 %
Local Thresholding3 %
Ilastik Headless (Pixel classification)3 %
Gaussian Convolution3 %
Sigma Filter3 %
Merger2 %
~~Table Row to Variable~~2 %
Anisotropic Diffusion2 %
Median Filter2 %
Image Normalizer2 %
Image Reader (Table)2 %
Global Thresholder2 %
Bilateral Filter2 %
~~Column Rename~~1 %
Image Converter1 %
Inverter1 %
Projector1 %
GroupBy1 %
Math Formula1 %
Image Cropper1 %
Image Calculator1 %
Concatenate1 %
Column Filter1 %
Max Filter1 %
Splitter1 %
Multilevel Thresholding1 %
Image Resizer1 %
Spot Detection1 %
Image to Labeling1 %
Interactive Annotator1 %
Image Reader1 %
Sobel Filter1 %
Variance Filter1 %
Smooth1 %
RowID< 1 %
ImageJ Macro< 1 %
Grayscale Reconstruction< 1 %
Distance Map< 1 %
Image Reader (Table) Remote< 1 %
Column Merger< 1 %
Sorter< 1 %
Image Features< 1 %
Convolver< 1 %
Binary Image Operations< 1 %
Labeling to Image< 1 %
Morphological Labeling Operations< 1 %
Group Loop Start< 1 %
Frangi Vesselness< 1 %
~~Table Column to Variable~~< 1 %
Column Aggregator< 1 %
Row Sampling< 1 %
Table Transposer< 1 %
Auto Crop< 1 %
IJ Image Reader (2D) - experimental< 1 %
Column Filter (legacy)< 1 %
Double Input (legacy)< 1 %
Segment Features< 1 %
Image Properties< 1 %
Splitter (uncropped)< 1 %
Labeling Filter< 1 %
Median< 1 %
Multiply...< 1 %
Column Resorter< 1 %
Rule-based Row Filter< 1 %
List Box Configuration< 1 %
Read Images< 1 %
~~File Reader~~< 1 %
~~Loop End~~< 1 %
~~Row Splitter (deprecated)~~< 1 %
Column Splitter< 1 %
String Replacer< 1 %
Integer Input (legacy)< 1 %
Average Filter< 1 %
Quantile Filter< 1 %
Image Generator< 1 %
Set Image Metadata< 1 %
Colorspace Converter< 1 %
h-Dome Extraction< 1 %
Morphological Image Operations< 1 %
Waehlby Cell Clump Splitter< 1 %
Adaptive Median< 1 %
Divide...< 1 %
Find Edges< 1 %
~~Generic Loop Start~~< 1 %
Column Appender< 1 %
Column Rename (Regex)< 1 %
Constant Value Column< 1 %
Cache< 1 %
Parallel Chunk Start< 1 %
Single Selection (legacy)< 1 %
Image Segment Features< 1 %
Max Homogeneity< 1 %
PNG Image to ImgPlus< 1 %
Labeling to RGB Img< 1 %
Align image< 1 %
Dimension Extender< 1 %
Local Maxima for Distance Map< 1 %
Fill Holes< 1 %
DoG Spot Detection< 1 %
Maximum Finder< 1 %
Seeded Watershed< 1 %
GraphCut 2D< 1 %
Voronoi Segmentation< 1 %
Don't Save Start< 1 %
Gaussian Blur...< 1 %
Invert...< 1 %
Read Image (IJ1)< 1 %
Sharpen< 1 %
Split Channels< 1 %
Tess4J< 1 %
R Snippet< 1 %
Split Collection Column< 1 %
CSV Reader< 1 %
Table Reader< 1 %
Chunk Loop Start< 1 %
Column to Grid< 1 %
String Manipulation< 1 %
Merge Variables< 1 %
Table View (JavaScript)< 1 %
Boolean Widget< 1 %
Data Row to Image< 1 %
Make Binary...< 1 %

Popular Successors

Views

Image Viewer: Another, possibly interactive, view on table cells. Displays the selected cells with their associated viewer if it exists. Available views are:
- Labeling View
-- View on a labeling/segmentation
- 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.
- XML
-- XML tree
- Histogram Viewer
-- This viewer shows the histogram of the currently selected image.
- Image Viewer
-- This viewer renders the selected image-cell.
- Missing Value Viewer
-- An empty viewer that is shown when the input cell has no value to display.
- 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.

Workflows

Developers

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Installation

To use this node in KNIME, install the extension KNIME Image Processing from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: University of Konstanz

Plugin version: 1.8.3.v202403231009

On NodePit since: 2024-07-11

Last update: 2024-11-21

Tags: Streamable

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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