Spaces:
Sleeping
Sleeping
File size: 1,662 Bytes
c75526e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | # 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
```python
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
|