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Example_​workflow

Import(images, metadata and ground truth) Query according to metadata(Year, Disease and Lighting) Normalization(Using ImageJ integration) Threshold(With the image processing Knime extension) PNG conversion Save images Dice calculation(Using a Python script) Add GT Statistical tests to compare ourthreshold with the GT(Using a R script)So that we can determine if themodel used for the GT is betterthan a simple threshold. Other intresting nodesGet node execution durationConnect to OMERO to retrieve your images (but only available for OMEROversion less than 5.2 while the current is 5.6.1) Knime workflow example for image processingIn this walkthrough you will see how to use image processing Knime nodes and how to usedifferent programming languages.Aurélien VALENTIN for the ImHorPhen research team (Angers, France) - July 2023 Import imagesImport metadataMerge tablesSplit channelsThreshol channelsAND operationAND operationRemoveRenameView resultRenameInto PNG objectsMerge tablesImport GTExtract valuesRemove ".png" in file namesKeep needed columnsMetanode with JavaScriptSave imagesView resultView resultView resultView resultImage Reader CSV Reader Joiner Splitter Global Thresholder Binary ImageOperations Binary ImageOperations Column Filter Column Rename Image Viewer Timer Info OMERO Reader (5.2) ImageJ Macro Column Rename ImgPlus toPNG Images Joiner Image Reader Column Rename Python Script(Labs) R Snippet Split CollectionColumn Column Expressions Column Filter Process query Image Writer(Table) Image Viewer Image Viewer Image Viewer Image Viewer Import(images, metadata and ground truth) Query according to metadata(Year, Disease and Lighting) Normalization(Using ImageJ integration) Threshold(With the image processing Knime extension) PNG conversion Save images Dice calculation(Using a Python script) Add GT Statistical tests to compare ourthreshold with the GT(Using a R script)So that we can determine if themodel used for the GT is betterthan a simple threshold. Other intresting nodesGet node execution durationConnect to OMERO to retrieve your images (but only available for OMEROversion less than 5.2 while the current is 5.6.1) Knime workflow example for image processingIn this walkthrough you will see how to use image processing Knime nodes and how to usedifferent programming languages.Aurélien VALENTIN for the ImHorPhen research team (Angers, France) - July 2023 Import imagesImport metadataMerge tablesSplit channelsThreshol channelsAND operationAND operationRemoveRenameView resultRenameInto PNG objectsMerge tablesImport GTExtract valuesRemove ".png" in file namesKeep needed columnsMetanode with JavaScriptSave imagesView resultView resultView resultView resultImage Reader CSV Reader Joiner Splitter Global Thresholder Binary ImageOperations Binary ImageOperations Column Filter Column Rename Image Viewer Timer Info OMERO Reader (5.2) ImageJ Macro Column Rename ImgPlus toPNG Images Joiner Image Reader Column Rename Python Script(Labs) R Snippet Split CollectionColumn Column Expressions Column Filter Process query Image Writer(Table) Image Viewer Image Viewer Image Viewer Image Viewer

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

Download Workflow
Created by: g-lar
Created at: 2023-07-26
On NodePit since: 2023-07-27
Last update: 2024-12-26
Created with KNIME version: v4.6.5

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