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04. Image Processing

Image Processing

"Image Processing" exercise for basic Life Science User Training
- smooth the image to reduce image noise using Gaussian convolution
- determine the foreground/bachkground threshold
- segment cells and apply labels
- split clumps of cells
- remove cell from image border
- calculate the features of each cell


Activity: Image ProcessingAim: calculate the size of each cell- use the Gaussian Convolution node to smooth your image to redcue image noise- use the Global Thresholder node utilizing the Otsu thresholding method- the Connected Component Analysis node segmentates the cells from the background and applies labels. In the Column Selection tab, make sure to append the new column.- the Waehlby Cell Clump Splitter node is used to segment clumps of cells. In the Column Selection tab, select "Replace first column" to replace the Segmentation column.- use the Labeling Filter node to remove cells on the image border (enable: remove segments toughing the border). In the Column Selection tab, select "Replace" to replace theSegmentation column.- the Image Segmentation Feature node can be used to calculate the size of the cells. In the Features tab, select "First Order Statistics" and select "Sum". synthetic cellimages List Files/Folders Image Reader(Table) Path to String Activity: Image ProcessingAim: calculate the size of each cell- use the Gaussian Convolution node to smooth your image to redcue image noise- use the Global Thresholder node utilizing the Otsu thresholding method- the Connected Component Analysis node segmentates the cells from the background and applies labels. In the Column Selection tab, make sure to append the new column.- the Waehlby Cell Clump Splitter node is used to segment clumps of cells. In the Column Selection tab, select "Replace first column" to replace the Segmentation column.- use the Labeling Filter node to remove cells on the image border (enable: remove segments toughing the border). In the Column Selection tab, select "Replace" to replace theSegmentation column.- the Image Segmentation Feature node can be used to calculate the size of the cells. In the Features tab, select "First Order Statistics" and select "Sum". synthetic cellimages List Files/Folders Image Reader(Table) Path to String

Nodes

Extensions

Links

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: janinamothes
Created at: 2021-04-30
On NodePit since: 2022-05-06
Last update: 2024-11-18
Created with KNIME version: v4.4.0
Tags: life scienceeducationimage processingcell featuressegmentation

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