Interactive visualization of phenotypic features in zebrafish

Workflow

Interactive visualization of phenotypic features in zebrafish

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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

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