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Channel Shift (3 Channels) Measurement and Track Correction

This workflow measures channel shift (caused by chromatic aberration and/or camera misalignment) from 3-channel images of fluorescent beads, and applies the measured transformation to correct track coordinates.

It requires the ‘FMI KNIME Plugins’ extension from the following update site:
https://community.knime.org/download/ch.fmi.knime.plugins.update/

Channel Shift Measurement and Track CorrectionThis workflow was created for the research group of Luca Giorgettiby Jan Eglinger, Friedrich Miescher Institute for Biomedical Research (FMI), BaselIn order to use this workflow, please make sure you installed the following extensions:- FMI KNIME Plugins from the FMI update site: https://community.knime.org/download/ch.fmi.knime.plugins.update/- KNIME Image Processing - ImageJ Integration- KNIME Interactive R Statistics Integration- KNIME Nodes for Wide Data (many columns)Note for Mac OSX users:to select a directory in the file chooser dialog (when configuring the output folder), navigate to the parent folder,then select the target folder (but don't double-click) and click Choose. Quality control:Plot distances between bead positions Choose input folder for bead images Adjust detection parameters for each channel ifnecessary Choose input folder for trajectories(xml files) Choose output folder for corrected xml Configure pixel spacingand output location Selectbead imageinput folderChannel 1 coordinatesChannel 2 coordinatesChannel 3 coordinatesSelect tracksinput folderList Files Spot Detection (Subpixellocalization) Spot Detection (Subpixellocalization) Spot Detection (Subpixellocalization) List Files Read images andsplit channels Match Correspondencesand Measure Transform Quality Control Configure Spacingand Output Folder Correct TrackingCoordinates Channel Shift Measurement and Track CorrectionThis workflow was created for the research group of Luca Giorgettiby Jan Eglinger, Friedrich Miescher Institute for Biomedical Research (FMI), BaselIn order to use this workflow, please make sure you installed the following extensions:- FMI KNIME Plugins from the FMI update site: https://community.knime.org/download/ch.fmi.knime.plugins.update/- KNIME Image Processing - ImageJ Integration- KNIME Interactive R Statistics Integration- KNIME Nodes for Wide Data (many columns)Note for Mac OSX users:to select a directory in the file chooser dialog (when configuring the output folder), navigate to the parent folder,then select the target folder (but don't double-click) and click Choose. Quality control:Plot distances between bead positions Choose input folder for bead images Adjust detection parameters for each channel ifnecessary Choose input folder for trajectories(xml files) Choose output folder for corrected xml Configure pixel spacingand output location Selectbead imageinput folderChannel 1 coordinatesChannel 2 coordinatesChannel 3 coordinatesSelect tracksinput folderList Files Spot Detection (Subpixellocalization) Spot Detection (Subpixellocalization) Spot Detection (Subpixellocalization) List Files Read images andsplit channels Match Correspondencesand Measure Transform Quality Control Configure Spacingand Output Folder Correct TrackingCoordinates

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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: eglijan
Created at: 2019-05-02
On NodePit since: 2020-06-17
Last update: 2024-12-21
Created with KNIME version: v4.0.2
Tags: chromatic-aberrationchannel-shift-correctionimagej

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