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IdentifyNuclei_​measure2Channels

IdentifyNuclei_measure2ChannelsThis workflow searches all tif files in a directory, identifies the cell nuclei in these. Based on the nucleisegmentation further recognition steps for instance for cytoplasmic regions based on the other colorchannels 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 needidentified nuclei to work correctly. you canplace as many as you need after the 'imageprocessing' metanode. copy as many feature calculation metanodes in yourworkflow as needed. Rmember to connect them with ajoiner, as in the example below. You can vizualize any of your intermediate results.Please specify the objects and the images in themetanode. With these nodes you can assign classes based onone mean value for the given objects. You can haveas many classes as you want by connecting mutipleassignment 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 forBioinformatics Infrastructure (HD.HuB as part of de.NBI; grant 031A537C).Please consider visiting https://www.denbi.de for mor information and possibly interestingtools and services! Saving of the results is rather specific here. You need to adapt it to your use-case! Threshould auf nuclei einstellen? https://kni.me/w/-PFtac7jHAEHn0Xd plaese specify thelocation of your fileshere!Node 708Node 742Node 744Node 773Node 776 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 865Node 866Node 867Node 868Node 869Node 870Node 871Node 872FilenameParserScanR List Files(deprecated) Sorter GroupBy String Manipulation Excel Writer (XLS)(deprecated) Excel Sheet Appender(XLS) (deprecated) 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 Sheet Appender(XLS) (deprecated) GroupByClassCombinations FilterObjectsByThreshold VoronoyExtendObjects CalculateFeatures Joiner CalculateFeatures ClassAssignement Group Loop Start GroupBy Row Filter Excel Sheet Appender(XLS) (deprecated) Joiner Math Formula Column Rename Excel Writer (XLS)(deprecated) IdentifyNuclei_measure2ChannelsThis workflow searches all tif files in a directory, identifies the cell nuclei in these. Based on the nucleisegmentation further recognition steps for instance for cytoplasmic regions based on the other colorchannels 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 needidentified nuclei to work correctly. you canplace as many as you need after the 'imageprocessing' metanode. copy as many feature calculation metanodes in yourworkflow as needed. Rmember to connect them with ajoiner, as in the example below. You can vizualize any of your intermediate results.Please specify the objects and the images in themetanode. With these nodes you can assign classes based onone mean value for the given objects. You can haveas many classes as you want by connecting mutipleassignment 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 forBioinformatics Infrastructure (HD.HuB as part of de.NBI; grant 031A537C).Please consider visiting https://www.denbi.de for mor information and possibly interestingtools and services! Saving of the results is rather specific here. You need to adapt it to your use-case! Threshould auf nuclei einstellen? https://kni.me/w/-PFtac7jHAEHn0Xd plaese specify thelocation of your fileshere!Node 708Node 742Node 744Node 773Node 776 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 865Node 866Node 867Node 868Node 869Node 870Node 871Node 872FilenameParserScanR List Files(deprecated) Sorter GroupBy String Manipulation Excel Writer (XLS)(deprecated) Excel Sheet Appender(XLS) (deprecated) 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 Sheet Appender(XLS) (deprecated) GroupByClassCombinations FilterObjectsByThreshold VoronoyExtendObjects CalculateFeatures Joiner CalculateFeatures ClassAssignement Group Loop Start GroupBy Row Filter Excel Sheet Appender(XLS) (deprecated) Joiner Math Formula Column Rename Excel Writer (XLS)(deprecated)

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Created by: manu
Created at: 2018-08-21
On NodePit since: 2021-06-11
Last update: 2024-12-17
Created with KNIME version: v4.3.2

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