PhaseContrastNeuriteAnalyzer

PhaseContrastNeuriteAnalyzer is a browser-guided software workflow for reproducible neurite analysis in phase-contrast microscopy images of SH-SY5Y cells. The tool integrates Bash launchers, Fiji/ImageJ macros, ilastik pixel classification, R-based cutoff optimization, production image analysis, and downstream statistical visualization through a Shiny-style interface designed for users with limited terminal experience. The workflow supports image preprocessing, ilastik-based segmentation, segmentation-label verification, validation-image grouping, manual inspection, ROI and skeleton extraction, reusable cutoff-profile optimization, application of selected cutoff models to larger image sets, metadata-aware visualization, dimensionality reduction, covariate inspection, grouped plots, ANCOVA-style analysis, and reproducible report generation.