data/docs_cache/openproblems_docs.md

OpenProblems Framework Guide

Overview

OpenProblems is a community effort to benchmark single-cell and spatial transcriptomics methods.

Project Architecture

Repository Structure

src/
├── tasks/                    # Benchmark tasks
│   ├── spatial_decomposition/
│   │   ├── methods/         # Benchmark methods
│   │   ├── metrics/         # Evaluation metrics
│   │   └── datasets/        # Task datasets
│   └── other_tasks/
├── common/                  # Shared components
└── workflows/              # Nextflow workflows

Component Types

Dataset Components

Load benchmark datasets with standardized formats.

Method Components

Implement spatial analysis methods following OpenProblems standards.

Metric Components

Evaluate method performance with standardized metrics.

Data Formats

AnnData Structure

import anndata as ad

# Spatial data structure
adata_spatial = ad.read_h5ad('spatial_data.h5ad')
# adata_spatial.X: expression matrix
# adata_spatial.obs: spot metadata
# adata_spatial.var: gene metadata
# adata_spatial.obsm['spatial']: spatial coordinates

# Reference single-cell data
adata_reference = ad.read_h5ad('reference_data.h5ad')
# adata_reference.obs['cell_type']: cell type annotations

Standard Metadata Fields

• Cell types: obs['cell_type']
• Spatial coordinates: obsm['spatial']
• Batch information: obs['batch']

Best Practices

• Follow OpenProblems naming conventions
• Use standard data formats (AnnData h5ad)
• Include comprehensive documentation
• Ensure reproducibility across platforms