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Counting OL

Counting oligodendrocytes

Counting oligodendrocytes

This tutorial workflow shows a High-content screening workflow. Of course parameters and methods have to be adjusted for your problem, but this is a good starting point.

General InformationPress the green double arrow above to run the complete workflow. To see the contents of a meta node (grey nodes) you can Double-Click on it, which opens a new tab with the nodes contained in this meta node.Workflow Description:This workflow shows a High-content screening workflow to count oligodendrocytes. Adapted from this workflow: https://hub.knime.com/knime/spaces/Examples/latest/99_Community/01_Image_Processing/03_Applications/06_High_Content_Screening~EZeNcsCyItk9fQ07 created by Christian Dietz.Workflow Requirements:KNIME Image Processing 1.8.3R software with Rserve and ggplot2 packagesWorkflow updated on 06/07/2021 1. Load images Count the number oflabels, hence, count thenumber of cells.Node 109oligo countingNode 135Node 136Node 137Node 138Node 139Node 143Remove imageextensionIntroduce parent folder with all tested concentrationsNode 147Node 148Node 552Node 554join nameNode 570Node 571Node 572Node 1734Node 1874Extracts first foldername to used in xls nameMEANSEMNode 1879Node 1880 Labeling Properties Labeling Properties Feature Extraction Segmentation InteractiveSegmentation View Preprocessing GroupBy Joiner Column Rename Math Formula GroupBy Joiner Labeling Properties R View (Table) String Manipulation List Files/Folders Table Row ToVariable Loop Start List Files/Folders Distributionof images Loop End (2 ports) Joiner Extract treatmentand concentration Excel Writer Image To Table String to Path(Variable) Table Rowto Variable Excel name GroupBy Math Formula InteractiveSegmentation View Concatenate Labeling Properties General InformationPress the green double arrow above to run the complete workflow. To see the contents of a meta node (grey nodes) you can Double-Click on it, which opens a new tab with the nodes contained in this meta node.Workflow Description:This workflow shows a High-content screening workflow to count oligodendrocytes. Adapted from this workflow: https://hub.knime.com/knime/spaces/Examples/latest/99_Community/01_Image_Processing/03_Applications/06_High_Content_Screening~EZeNcsCyItk9fQ07 created by Christian Dietz.Workflow Requirements:KNIME Image Processing 1.8.3R software with Rserve and ggplot2 packagesWorkflow updated on 06/07/2021 1. Load images Count the number oflabels, hence, count thenumber of cells.Node 109oligo countingNode 135Node 136Node 137Node 138Node 139Node 143Remove imageextensionIntroduce parent folder with all tested concentrationsNode 147Node 148Node 552Node 554join nameNode 570Node 571Node 572Node 1734Node 1874Extracts first foldername to used in xls nameMEANSEMNode 1879Node 1880 Labeling Properties Labeling Properties Feature Extraction Segmentation InteractiveSegmentation View Preprocessing GroupBy Joiner Column Rename Math Formula GroupBy Joiner Labeling Properties R View (Table) String Manipulation List Files/Folders Table Row ToVariable Loop Start List Files/Folders Distributionof images Loop End (2 ports) Joiner Extract treatmentand concentration Excel Writer Image To Table String to Path(Variable) Table Rowto Variable Excel name GroupBy Math Formula InteractiveSegmentation View Concatenate Labeling Properties

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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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On NodePit since: 2022-07-14
Last update: 2024-11-17
Created with KNIME version: v4.3.3

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