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yh2ax

Foci Segmentation Nuclei Segmentation Just for initial visualization This excludes specific rows of aplate and also selects specificcolumns for analysis.TODO Get this from theexperiment definition Using yH2AX for detection of foci Using regular image processing for nuclei segmentation Filter out nuclei according tosome criteria TODO We need to get this from theexperimemnt description I guess TODO Enable streaming so that the downloadisn't blockingTODO Check if download of images wassuccessful Since most of the images will be stiched, there will be no size thatis applicable to all images. Hence, we'll have to process themindividually Upload masks for report as assets using arctoris-client Using machine learning for nuclei segmentation Using deep learning for nuclei segmentation Merge nuclei andfoci labeling imagesCompute containingnucleus for eachfocusRename labelsto Foci_XCount foci pernucleusGet original filenameDrop DAPIDrop yH2AXCompute averagefoci count per wellWell position toconcentrationmappingRename labelsto Nuclei_XExclude outliersper wellOnly keep focibetween 3 and 10pxNode 94Machine Learning-basednuclei segmentationDrop yH2AXThreshold probabilityimage for nucleiSplit resultingprobability imagesFill holes in nucleijust in caseGet filenamesUse filenamesas rowIDsPresigned S3 URLsDownload all imagesinto a temporary folderLoad modelFigure outfile pairs frominput listOverall segmentationsNode 145Filtered nucleireplace the old nucleilabeling imagesExtract well&rowProvide meaningfulnames for columnsavg-foci-countsAdd unitNode 316Node 320parametersFilename mappingUse filename mappingCompute targetlocation for downloadCompute"certainty"per nucleusNode 344Sample cells(stratified on the bins)Normalize s.t.the nuclei areactually visibleBin into 5 binsWrite Image Maskinto PNG fileCreate a temporarydirectory for the outputimagesPut into one ZIPAll output imagesLoginDummy tableNode 399Upload asset andreturn hash in outputDynamically createthe commandline callfor asset uploadingexperiment-idNode 423Node 424Get dimensionsNode 439Node 440Node 441nuclei-segmentationTranslate toport selectionTensorFlow zippedSavedModelsegmentation-masksExtract filename basefrom RowIDAdd extensionNode 468Node 470Join withasset hashReconstruct RowIDCreates a collection fromthe cell mask filenamesIndividual cellsSample cellsfor reportSample cellsfor reportNode 486Node 487environmentNode 489upload-usernameupload-passwordNode 492Cell Replacer Spot Detection Connected ComponentAnalysis Merger Image Viewer GaussianConvolution Global Thresholder Connected ComponentAnalysis Joiner Labeling Arithmetic Segment Features Label Transformer GroupBy Labeling Properties Column Filter Column Filter GroupBy Data Preparation Model Execution Table Creator Label Transformer Joiner Numeric Outliers Massage listof image files Labeling Filter Image Reader(Table) Column Rename Column Filter Ilastik Headless(Pixel classification) Column Filter Global Thresholder Splitter Column Filter Connected ComponentAnalysis Fill Holes Column Rename Image Properties RowID ContainerInput (JSON) JSON Path Download /Upload from List Ungroup Create Temp Dir String to URI TensorFlowNetwork Reader Cleaning Up Pivoting CASE SwitchData (End) Split nuclei CASE SwitchData (Start) Column Rename Filter nuclei Regex Split Column Rename Visualize results String To Number Table to JSON ContainerOutput (JSON) ConstantValue Column Column Resorter IF Switch Column Rename Column Filter GroupBy Variable toTable Row Table to JSON ContainerOutput (JSON) Unify segmentationoutput Unify segmentationoutput ContainerInput (JSON) JSON Path Ungroup Cell Replacer Java Snippet Image SegmentFeatures Joiner Row Sampling Image Normalizer Auto-Binner Overlap imagesfrom cell masks Image Writer(Table Column) Create Temp Dir Zip Files List Files ExternalTool (Labs) Table Creator Create Temp Dir ExternalTool (Labs) Merge Variables String Manipulation(Variable) String Input Crop Images Chunk Loop Start Loop End Labeling to RGB Img Image Properties String Manipulation RowID Image Writer String Input Java Edit Variable File Upload ContainerOutput (JSON) RowID String Manipulation Joiner Table to JSON RowID Cross Joiner RowID Convert toabsolute path Collect file names Create dummy files forExternal Tool nodes Unify segmentationoutput CASE SwitchData (End) Row Sampling Segment Features Segment Features Row Sampling Asset hash from URL Run GarbageCollector String Manipulation(Variable) String Input Merge Variables String Input String Input Merge Variables Foci Segmentation Nuclei Segmentation Just for initial visualization This excludes specific rows of aplate and also selects specificcolumns for analysis.TODO Get this from theexperiment definition Using yH2AX for detection of foci Using regular image processing for nuclei segmentation Filter out nuclei according tosome criteria TODO We need to get this from theexperimemnt description I guess TODO Enable streaming so that the downloadisn't blockingTODO Check if download of images wassuccessful Since most of the images will be stiched, there will be no size thatis applicable to all images. Hence, we'll have to process themindividually Upload masks for report as assets using arctoris-client Using machine learning for nuclei segmentation Using deep learning for nuclei segmentation Merge nuclei andfoci labeling imagesCompute containingnucleus for eachfocusRename labelsto Foci_XCount foci pernucleusGet original filenameDrop DAPIDrop yH2AXCompute averagefoci count per wellWell position toconcentrationmappingRename labelsto Nuclei_XExclude outliersper wellOnly keep focibetween 3 and 10pxNode 94Machine Learning-basednuclei segmentationDrop yH2AXThreshold probabilityimage for nucleiSplit resultingprobability imagesFill holes in nucleijust in caseGet filenamesUse filenamesas rowIDsPresigned S3 URLsDownload all imagesinto a temporary folderLoad modelFigure outfile pairs frominput listOverall segmentationsNode 145Filtered nucleireplace the old nucleilabeling imagesExtract well&rowProvide meaningfulnames for columnsavg-foci-countsAdd unitNode 316Node 320parametersFilename mappingUse filename mappingCompute targetlocation for downloadCompute"certainty"per nucleusNode 344Sample cells(stratified on the bins)Normalize s.t.the nuclei areactually visibleBin into 5 binsWrite Image Maskinto PNG fileCreate a temporarydirectory for the outputimagesPut into one ZIPAll output imagesLoginDummy tableNode 399Upload asset andreturn hash in outputDynamically createthe commandline callfor asset uploadingexperiment-idNode 423Node 424Get dimensionsNode 439Node 440Node 441nuclei-segmentationTranslate toport selectionTensorFlow zippedSavedModelsegmentation-masksExtract filename basefrom RowIDAdd extensionNode 468Node 470Join withasset hashReconstruct RowIDCreates a collection fromthe cell mask filenamesIndividual cellsSample cellsfor reportSample cellsfor reportNode 486Node 487environmentNode 489upload-usernameupload-passwordNode 492Cell Replacer Spot Detection Connected ComponentAnalysis Merger Image Viewer GaussianConvolution Global Thresholder Connected ComponentAnalysis Joiner Labeling Arithmetic Segment Features Label Transformer GroupBy Labeling Properties Column Filter Column Filter GroupBy Data Preparation Model Execution Table Creator Label Transformer Joiner Numeric Outliers Massage listof image files Labeling Filter Image Reader(Table) Column Rename Column Filter Ilastik Headless(Pixel classification) Column Filter Global Thresholder Splitter Column Filter Connected ComponentAnalysis Fill Holes Column Rename Image Properties RowID ContainerInput (JSON) JSON Path Download /Upload from List Ungroup Create Temp Dir String to URI TensorFlowNetwork Reader Cleaning Up Pivoting CASE SwitchData (End) Split nuclei CASE SwitchData (Start) Column Rename Filter nuclei Regex Split Column Rename Visualize results String To Number Table to JSON ContainerOutput (JSON) ConstantValue Column Column Resorter IF Switch Column Rename Column Filter GroupBy Variable toTable Row Table to JSON ContainerOutput (JSON) Unify segmentationoutput Unify segmentationoutput ContainerInput (JSON) JSON Path Ungroup Cell Replacer Java Snippet Image SegmentFeatures Joiner Row Sampling Image Normalizer Auto-Binner Overlap imagesfrom cell masks Image Writer(Table Column) Create Temp Dir Zip Files List Files ExternalTool (Labs) Table Creator Create Temp Dir ExternalTool (Labs) Merge Variables String Manipulation(Variable) String Input Crop Images Chunk Loop Start Loop End Labeling to RGB Img Image Properties String Manipulation RowID Image Writer String Input Java Edit Variable File Upload ContainerOutput (JSON) RowID String Manipulation Joiner Table to JSON RowID Cross Joiner RowID Convert toabsolute path Collect file names Create dummy files forExternal Tool nodes Unify segmentationoutput CASE SwitchData (End) Row Sampling Segment Features Segment Features Row Sampling Asset hash from URL Run GarbageCollector String Manipulation(Variable) String Input Merge Variables String Input String Input Merge Variables

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Created by: helfrich
Created at: 2019-06-05
On NodePit since: 2024-11-19
Last update: 2024-12-21
Created with KNIME version: v4.1.3

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