Mievformer

Getting Started

  • Installation
    • Requirements
      • Optional Dependencies
    • Installation via pip
    • Installation from source
    • GPU Support
    • Docker Installation
      • Building the Docker Image
      • Running with GPU Support
      • Running the Tutorial
      • Interactive Mode
    • Troubleshooting
      • NumPy Compatibility
      • Missing igraph/leidenalg
      • TensorBoard Not Found
    • Verifying Installation
  • Getting Started: Single-Slice Analysis
    • 1. Create spatial data
    • 2. Train and calculate the standard CA view
    • 3. Downstream density-ratio analysis
  • Multi-Batch Analysis
    • Prepare the AnnData object
    • Run sample-conditional Mievformer CA
    • Multi-batch output contract

User Guide

  • Overview of Mievformer
    • Abstract
    • Methodology
      • Input Data Preparation and Model Optimization
      • Algorithm
      • Multiple Spatial Slices
      • Downstream Analyses
  • API Reference
    • Core Model Functions
      • optimize_nicheformer()
      • calculate_wb_ez()
    • Niche Density Ratio and Membership
      • calculate_niche_density_ratio()
      • calculate_niche_cluster_membership()
    • Downstream Analysis
      • estimate_population_density()
      • analyze_density_correlation()
      • analyze_niche_membership()

About

  • Release Notes
    • Version 0.3.0 (2026)
      • Changed
      • Added
      • Removed
      • Compatibility
    • Version 0.2.0 (2026)
      • Changed (Breaking — API rename for semantic clarity)
      • Fixed
      • Preserved
      • Added
    • Version 0.1.0 (2025)
      • Features
      • Documentation
  • References
    • Citing Mievformer
    • Related Work
      • Spatial Transcriptomics Methods
      • Deep Learning Frameworks
      • Single-Cell Analysis
    • Contact
Mievformer
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