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Raw_​Thickness_​Maps

Raw Thickness Map Workflow**This workflow was written by Ellen Arena (LOCI, earena@wisc.edu) and Marcel Wiedenmann(KNIME, marcel.wiedenmann@knime.com) in June 2019.NOTE: If running Automatic method on a Windows machine, a Fiji window will be opennedduring the run and a log window will also pop up... just let it run without interfering (ie do not'click' on anything) as it will close on its own when finished. When on a Mac... Fiji will runheadlessly (ie you won't see a Fiji window appear when the KNIME workflow is running). To Start Workflow: 1) right click on "Input-Parameters" node and click 'Configure'2) set all input parametersIf "Automatic" method chosen... 3) right click on "Segmentation Area Measurements" node near the end of the workflow andclick 'Execute'If "Manual" method chosen...3) right click on "Generate Thickness Maps" node and click 'Execute'4) right click on "Interactive Annotator" node and click 'Configure'5) Move through each image, drawing regions of interest (ROI) using the polygon selectiontool (don't worry about staying within the ring when drawing... those regions outside will befiltered out for area calculations)6) once finished annotating all ROIs... right click on "Segmentation Area Measurements" nodenear the end of the workflow and click 'Execute'All final results of the segmentations can be inspected by running the "InteractiveSegmentation View" node at the end of the workflow (right click and select "Execute and OpenViews" and then double-click on an image). visual check of segmentationssaves label masks using TWSManual Segmentationsaves thickness maps and center circle maskssaves segmented masksand area measurements InteractiveSegmentation View Input-Parameters AutomaticSegmentation InteractiveAnnotator GenerateThickness Maps Segmentation AreaMeasurements Raw Thickness Map Workflow**This workflow was written by Ellen Arena (LOCI, earena@wisc.edu) and Marcel Wiedenmann(KNIME, marcel.wiedenmann@knime.com) in June 2019.NOTE: If running Automatic method on a Windows machine, a Fiji window will be opennedduring the run and a log window will also pop up... just let it run without interfering (ie do not'click' on anything) as it will close on its own when finished. When on a Mac... Fiji will runheadlessly (ie you won't see a Fiji window appear when the KNIME workflow is running). To Start Workflow: 1) right click on "Input-Parameters" node and click 'Configure'2) set all input parametersIf "Automatic" method chosen... 3) right click on "Segmentation Area Measurements" node near the end of the workflow andclick 'Execute'If "Manual" method chosen...3) right click on "Generate Thickness Maps" node and click 'Execute'4) right click on "Interactive Annotator" node and click 'Configure'5) Move through each image, drawing regions of interest (ROI) using the polygon selectiontool (don't worry about staying within the ring when drawing... those regions outside will befiltered out for area calculations)6) once finished annotating all ROIs... right click on "Segmentation Area Measurements" nodenear the end of the workflow and click 'Execute'All final results of the segmentations can be inspected by running the "InteractiveSegmentation View" node at the end of the workflow (right click and select "Execute and OpenViews" and then double-click on an image). visual check of segmentationssaves label masks using TWSManual Segmentationsaves thickness maps and center circle maskssaves segmented masksand area measurements InteractiveSegmentation View Input-Parameters AutomaticSegmentation InteractiveAnnotator GenerateThickness Maps Segmentation AreaMeasurements

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Created by: ellenarena
Created at: 2019-05-31
On NodePit since: 2020-01-30
Last update: 2024-04-25
Created with KNIME version: v4.1.0

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