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NucleiClassificationTraining

Nuclei Classification Trainig

This workflow reads images from a high throughput experiment acquired with an Olympus ScanR Microscope. A subset of the image data is used to train a classifier, which is then applied to the whole data set. A classifier is trained on exemplary images and applied to the whole dataset.



NucleiClassification* example data can be found under the link in the description.* in the List Files Node specify the directory you want to work with.* select images with the two row filters in order to train a classifier. At the moment, the first row filter selects a certain subposition, the second a specific row.* open the Labeling Editor and define a training set by creating new classes and clicking on the according objects in the image. Refer to the help of the node for details.* run the rest of the workflow to classify the whole dataset.* Configure the Excel Writer to save your data accordingly. de.NBI Acknowledgement:If you like this workfllow and want to acknowledge it in your work, please do so! This workflow was composed by Manuel Gunkel (manuel.gunkel@bioquant.uni-heidelberg.de) as partof the German Network for Bioinformatics Infrastructure (HD.HuB as part of de.NBI; grant 031A537C).Please consider visiting https://www.denbi.de for more information and interesting tools and services!Please consider also giving us feedback via the Surveymonkey link in the description, or visit https://www.surveymonkey.de/r/denbi-service?sc=hd-hub&tool=knime-cell to do so. It's really really short just three questions, remarks and comments are optional.Many Thanks!! Copy Image Processing and Feature Extraction from the training branch above down to theprocessing branch and reconnect them as shown below, in order to have the same processing steps!(delete the nodes below beforehand or afterwards!) || || \/ \/ Node 1select subpos rangeselect ID rangeNode 842Node 845Node 846Node 853Node 866Node 874Node 875Node 879Node 881Node 884Node 887Node 889Image Processing List Files Row Filter Row Filter Excel Reader (XLS)(deprecated) Joiner ConditionalBox Plot Joiner Normalization Object Counting Metadata Handling Random ForestLearner Random ForestPredictor Row Filter Plate HeatmapViewer RowID Z-Primes (PC x NC) Excel Writer (XLS)(deprecated) Plate Info InteractiveLabeling Editor Image Processing Feature Extraction Feature Extraction FilenameParserScanR NucleiClassification* example data can be found under the link in the description.* in the List Files Node specify the directory you want to work with.* select images with the two row filters in order to train a classifier. At the moment, the first row filter selects a certain subposition, the second a specific row.* open the Labeling Editor and define a training set by creating new classes and clicking on the according objects in the image. Refer to the help of the node for details.* run the rest of the workflow to classify the whole dataset.* Configure the Excel Writer to save your data accordingly. de.NBI Acknowledgement:If you like this workfllow and want to acknowledge it in your work, please do so! This workflow was composed by Manuel Gunkel (manuel.gunkel@bioquant.uni-heidelberg.de) as partof the German Network for Bioinformatics Infrastructure (HD.HuB as part of de.NBI; grant 031A537C).Please consider visiting https://www.denbi.de for more information and interesting tools and services!Please consider also giving us feedback via the Surveymonkey link in the description, or visit https://www.surveymonkey.de/r/denbi-service?sc=hd-hub&tool=knime-cell to do so. It's really really short just three questions, remarks and comments are optional.Many Thanks!! Copy Image Processing and Feature Extraction from the training branch above down to theprocessing branch and reconnect them as shown below, in order to have the same processing steps!(delete the nodes below beforehand or afterwards!) || || \/ \/ Node 1select subpos rangeselect ID rangeNode 842Node 845Node 846Node 853Node 866Node 874Node 875Node 879Node 881Node 884Node 887Node 889Image Processing List Files Row Filter Row Filter Excel Reader (XLS)(deprecated) Joiner ConditionalBox Plot Joiner Normalization Object Counting Metadata Handling Random ForestLearner Random ForestPredictor Row Filter Plate HeatmapViewer RowID Z-Primes (PC x NC) Excel Writer (XLS)(deprecated) Plate Info InteractiveLabeling Editor Image Processing Feature Extraction Feature Extraction FilenameParserScanR

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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: manu
Created at: 2019-05-14
On NodePit since: 2019-11-08
Last update: 2026-01-10
Created with KNIME version: v4.1.4
Tags: HCSimage segmentationclassificationphenotypes

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