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Interactive visualization of phenotypic features in zebrafish

PCA Screening Zebrafish Javascript views Visualization
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This workflow allows to explore some features from a toxicity screening in zebrafish larvae. There are 10 morphological features describing the kidney morphology, correpsonding o manual measurements on microscopy images. The workflow displays the value for the features as a line plot for each compound, as well as a 3D PCA scatter plot for easier identification of similar compounds.

External resources

  • Youtube tutorial
  • Open-access article
  • PCA in the python data-science handbook
  • Download input table from biorxiv (suppl.software)
  • Download the input table from the open-science framework

Used extensions & nodes

Created with KNIME Analytics Platform version 4.2.1
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    KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.2

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    KNIME Excel Support Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.1

    knime
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    KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.1

    knime
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    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.0

    knime
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    KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.0

    knime
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    KNIME Plotly Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

    knime
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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.1

    knime
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