Icon

IdentifyNuclei_​measure2Channels

IdentifyNuclei_measure2ChannelsThis workflow searches all tif files in a directory, identifies the cell nuclei in these. Based on the nuclei segmentation further recognitionsteps for instance for cytoplasmic regions based on the other color channels can be performed.Mean intensities of the identified objects are measured.For information about the grey metanodes, doubleclick those and select the questionmark. These Metanodes are optional and need identified nuclei towork correctly. you can place as many as you need after the'image processing' metanode. copy as many feature calculation metanodes in your workflow as needed.Rmember to connect them with a joiner, as in the example below. You can vizualize any of your intermediate results. Please specify theobjects and the images in the metanode. With these nodes you can assign classes based on one mean valuefor the given objects. You can have as many classes as you want byconnecting mutiple assignment nodes. Here you can visualize the class assignments. 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 as part of the German Network for Bioinformatics Infrastructure (HD.HuB as part of de.NBI; grant 031A537C).Please consider visiting https://www.denbi.de for mor information and possibly interesting tools and services! Saving of the results is rather specific here. You need to adapt it to your use-case! plaese specify thelocation of your fileshere!Node 708Node 742Node 744Node 773Node 775Node 776Node 777 DOUBLE-CLICK TO CONFIGURENode 792 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 812 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 819filter out all imagesNode 828 DOUBLE-CLICK TO CONFIGURENode 839Node 844Node 845Node 846Node 847filter out all imagesNode 850Node 851Node 852Node 858 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 862 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 865FilenameParserScanR List Files Sorter GroupBy String Manipulation Excel Writer (XLS) Excel SheetAppender (XLS) Excel SheetAppender (XLS) Group Loop Start Image Processing InteractiveSegmentation View CalculateFeatures FilterObjectsByThreshold VoronoyExtendObjects Joiner Visualization CalculateFeatures Joiner Column Filter Row Filter ClassAssignement InteractiveSegmentation View Visualization-Grouped Group Loop Start Loop End Loop End (2 ports) Sorter Column Filter Joiner GroupBy Excel SheetAppender (XLS) GroupByClassCombinations FilterObjectsByThreshold VoronoyExtendObjects CalculateFeatures Joiner CalculateFeatures ClassAssignement InteractiveAnnotator IdentifyNuclei_measure2ChannelsThis workflow searches all tif files in a directory, identifies the cell nuclei in these. Based on the nuclei segmentation further recognitionsteps for instance for cytoplasmic regions based on the other color channels can be performed.Mean intensities of the identified objects are measured.For information about the grey metanodes, doubleclick those and select the questionmark. These Metanodes are optional and need identified nuclei towork correctly. you can place as many as you need after the'image processing' metanode. copy as many feature calculation metanodes in your workflow as needed.Rmember to connect them with a joiner, as in the example below. You can vizualize any of your intermediate results. Please specify theobjects and the images in the metanode. With these nodes you can assign classes based on one mean valuefor the given objects. You can have as many classes as you want byconnecting mutiple assignment nodes. Here you can visualize the class assignments. 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 as part of the German Network for Bioinformatics Infrastructure (HD.HuB as part of de.NBI; grant 031A537C).Please consider visiting https://www.denbi.de for mor information and possibly interesting tools and services! Saving of the results is rather specific here. You need to adapt it to your use-case! plaese specify thelocation of your fileshere!Node 708Node 742Node 744Node 773Node 775Node 776Node 777 DOUBLE-CLICK TO CONFIGURENode 792 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 812 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 819filter out all imagesNode 828 DOUBLE-CLICK TO CONFIGURENode 839Node 844Node 845Node 846Node 847filter out all imagesNode 850Node 851Node 852Node 858 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 862 DOUBLE-CLICK TO CONFIGURE DOUBLE-CLICK TO CONFIGURENode 865FilenameParserScanR List Files Sorter GroupBy String Manipulation Excel Writer (XLS) Excel SheetAppender (XLS) Excel SheetAppender (XLS) Group Loop Start Image Processing InteractiveSegmentation View CalculateFeatures FilterObjectsByThreshold VoronoyExtendObjects Joiner Visualization CalculateFeatures Joiner Column Filter Row Filter ClassAssignement InteractiveSegmentation View Visualization-Grouped Group Loop Start Loop End Loop End (2 ports) Sorter Column Filter Joiner GroupBy Excel SheetAppender (XLS) GroupByClassCombinations FilterObjectsByThreshold VoronoyExtendObjects CalculateFeatures Joiner CalculateFeatures ClassAssignement InteractiveAnnotator

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: Manu Gunkel
Created at: 2018-08-21
On NodePit since: 2019-05-07
Last update: 2024-04-19
Created with KNIME version: v3.7.2
NodePit Exclusive Only available on NodePit

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!