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Monitoring nucleolar-nucleoplasmic protein shuttling in living cells

This workflow can be used to analyze nucleolar-nucleoplasmic protein shuttling in living cells. For detailed information we refer to our recent study ('Monitoring nucleolar-nucleoplasmic protein shuttling in

IMPORTANT:
Before use, make sure that all missing extensions are installed.
For StarDist installation instructions, read https://forum.image.sc/t/stardist-or-noise2voide-from-knime/39117/4.
To run Ilastik in KNIME, please install the Image Processing Ilastik Integration and install Ilastik on your computer device. Then, go to File > Preferences >KNIME > Image Processing Plugin > Ilastik and make sure that the path to the Ilastik installation (Ilastik.exe) is right.

BUG FIXING:If you encounter an error while executing the 'Column Appender' node(Execute failed: Tables can't be joined, non matching row counts), gointo the 'Segmentation of Nucleoli' meta node and reset the 'GroupBy' node, then execute the rest of the workflow Reads in imagesChose directory, file name and sheet name Chose folder to readimages fromChose directory, file name and sheet name Image Reader Segmentationof Nuclei Segmentationof Nucleoli Subtract/MergeSegmentations Joiner Column Appender File pathmanipulation Data Pre-Processing Calculate MeanSiR-Hoechst intensity Excel Writer List Files/Folders Feature Extraction Excel Writer BUG FIXING:If you encounter an error while executing the 'Column Appender' node(Execute failed: Tables can't be joined, non matching row counts), gointo the 'Segmentation of Nucleoli' meta node and reset the 'GroupBy' node, then execute the rest of the workflow Reads in imagesChose directory, file name and sheet name Chose folder to readimages fromChose directory, file name and sheet name Image Reader Segmentationof Nuclei Segmentationof Nucleoli Subtract/MergeSegmentations Joiner Column Appender File pathmanipulation Data Pre-Processing Calculate MeanSiR-Hoechst intensity Excel Writer List Files/Folders Feature Extraction Excel Writer

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: moltox_8
Created at: 2024-07-09
On NodePit since: 2024-07-10
Last update: 2026-01-14
Created with KNIME version: v5.2.5

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