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04. Image Processing - solution

Image Processing

Solution to "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". threshold forforeground vs backgroundcell segmentationcell clump splittingremoving cells from image bordercalculatingcell sizesmoothingsynthetic cellimages List Files/Folders Global Thresholder Connected ComponentAnalysis Waehlby CellClump Splitter Labeling Filter Image SegmentFeatures GaussianConvolution 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". threshold forforeground vs backgroundcell segmentationcell clump splittingremoving cells from image bordercalculatingcell sizesmoothingsynthetic cellimages List Files/Folders Global Thresholder Connected ComponentAnalysis Waehlby CellClump Splitter Labeling Filter Image SegmentFeatures GaussianConvolution Image Reader(Table) Path to String

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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: v4.5.2
Tags: life scienceeducationimage processingcell featuressegmentation

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