CLAIREscope v1.0.1: UI Layout Optimizations, Dynamic Colormap Reactivity & Dataset Discovery

🚀 CLAIREscope v1.0.1 — Patch & UI Optimization Release

CLAIREscope v1.0.1 introduces major visual enhancements to static and interactive UMAP views, dynamic colormap synchronization, and automated project dataset discovery.

🎨 Visual & Layout Optimizations

• Full-Width Bottom Legend Layout: Resolved static UMAP plot shrinking caused by long or numerous cluster labels by defaulting legends underneath coordinate axes with dynamic multi-column wrapping.
• On-Data Centroid Cluster Labels: Added Seurat/Scanpy-style cluster label overlays at centroids with high-contrast halo strokes.
• Streamlined Layout Controls: Unified Static Grid controls into a clean 3-column toolbar (Grid Columns, Grid Rows, Legend Position).
• Dynamic Colormap Max Reactivity: Synchronized Colormap Max (vmax) with the Max Percentile Threshold (Anchors) slider and selected gene across Static UMAP, Interactive UMAP, and Heatmap views.
• Intelligent Auto-Highlighting: Subsetting clusters in Interactive UMAP automatically switches the view mode to "Highlight selected (dim unselected in grey)".
• Sortable Multiselect: Added draggable chips with Select All and Clear controls for cell state filtering.

📁 Ingestion & Stability Improvements

• Recursive Dataset Scanner: Automatically discovers all .h5ad files within project root directories (scan_project_datasets).
• Interactive Project Ingestion: Added "➕ New Project..." in the sidebar with drag-and-drop file upload and root directory auto-detection.
• Scanpy Scoring Fallback: Fixed ValueError: No valid genes were passed for scoring in compute_score via use_raw=False and variable validation.
• Dynamic Gallery Resolution: Fixed figure directory path resolution in Trajectory Analysis.

CLAIREscope v1.0.0: Initial Public Release

🔬 CLAIREscope v1.0.0 — Initial Public Release

We are excited to announce the initial public release of CLAIREscope (Single-Cell Cutaneous Landscape Analysis & Interactive Responsive Exploration platform), an open-source, high-throughput interactive visual analytics framework tailored for cutaneous biology, single-cell genomics, and multi-condition cohort comparisons.

🌟 Key Highlights & Exploration Modules

• 🎨 Static & Interactive UMAP Studios:
  • Side-by-side comparison grids with Loupe Browser-style Log2 scaling and anchor percentile contrast thresholds.
  • Interactive 2D & 3D hardware-accelerated Plotly WebGL viewer with customizable color schemes, point density, and 3D camera controls.
• 📊 Quantitative Cohort Analytics:
  • Sample Composition Studio: Proportional donut charts and stacked distributions with automated Fisher's exact / Chi-square test statistics.
  • Gene Expression Violins: Multi-gene distribution violins with automated non-parametric Mann-Whitney U test p-values.
  • Co-Expression & Correlation Studio: Bivariate scatter plots with linear regression, Pearson ($), and Spearman ($\rho$) correlation metrics.
• 🧬 Functional Genomics & Dynamics:
  • Signature & Pathway Scoring Studio: Built-in score generator for custom gene sets and cutaneous biology signatures.
  • Developmental Trajectory Analysis: Diffusion Pseudotime (DPT) curves, vector trajectories, and precomputed analysis galleries.
  • Differential Expression & Volcano Plot Studio: Interactive volcano plots with customizable $\log_2\text{FC}$ and $-value cutoffs.
  • Pathway Enrichment Studio: Hypergeometric over-representation analysis against curated Gene Ontology and pathway databases.
  • Expression Heatmap Studio: Publication-grade hierarchical clustered heatmaps with Z-score standardization.
• 🩺 Curated Cutaneous Biology Knowledgebase:
  • Integrated signature library spanning epidermal differentiation (Basal 1, Basal 2, Spinous, Granular), hair follicle compartments, fibroblast subpopulations, immune infiltrates, and wound healing cascades.
• 💻 Desktop Integration:
  • Native 1-click desktop launcher (CLAIREscope.bat) and Python Tkinter Server Manager GUI.
• 📜 Archival & Citation:
  • Official Zenodo DOI: 10.5281/zenodo.22308479.