We released PhaseContrastNeuriteAnalyzer, together with a 5.8-GB open microscopy dataset supporting its development and validation.
The workflow was created to make quantitative analysis of neurite-related morphology more accessible in experiments where cells are followed using standard phase-contrast microscopy. It integrates Fiji/ImageJ preprocessing, ilastik pixel classification and R-based analysis in a guided workflow designed for reproducible use.
The accompanying Zenodo dataset contains raw phase-contrast images, experimental metadata, ilastik training material and model files, example segmentation outputs and representative downstream analysis results from experiments with SH-SY5Y cells treated with rosmarinic and retinoic acid.
Publishing the images, analysis workflow and metadata together allows researchers not only to read the resulting scientific conclusions, but also to inspect how those conclusions were produced and to reuse the resources for method development or independent analyses.
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