feat: Integrate mantis-analysis-template as reusable pipeline templates

[tayllatheodoro]

Merges the mantis-analysis-template repository into biahub as a collection of reusable analysis pipeline templates. Includes three template variants for different microscopy workflows.

Templates Added

1. Mantis Template (templates/mantis/)

Complete pipeline for standard Mantis microscope workflows:

• Zarr conversion and data management
• Label-free phase reconstruction with waveorder
• Virtual staining with VisCy
• Light-sheet deskewing and deconvolution
• Multi-channel registration (manual/beads/ANTs)
• XYZ stabilization
• Cell tracking with ultrack
• Visualization and QC tools

2. Dragonfly Template (templates/dragonfly/)

Pipeline variant optimized for Dragonfly spinning disk confocal systems

• Similar structure to Mantis template
• Dragonfly-specific configurations and parameters

3. Zebrafish Physics Pipeline (templates/zebraphysics-mantis-pipeline/) Specialized pipeline for zebrafish developmental biology experiments:

• Extended drift analysis tools
• Physics-specific data processing
• Customized tracking parameters
• Additional SLURM batch configurations

New Features

Template CLI Commands

# List available templates
biahub template list

# Show template details
biahub template info mantis

# Initialize new project from template
biahub template init -t mantis -o ./my-project --dataset exp_001

Template Structure

Each template includes:

• 0-convert/: Data conversion and setup
• 1-preprocess/: Label-free and light-sheet preprocessing
• 2-assemble/: Data assembly and concatenation
• 3-visualization/: Visualization and QC scripts
• run_pipeline.py: Pipeline orchestration
• check_logs.py: SLURM log monitoring
• README.md: Complete documentation

Files Added

• templates/ - New templates directory with all three templates (~250 files)
• biahub/cli/template_manager.py - Template management CLI
• templates/README.md - Templates overview and usage guide
• MANTIS_TEMPLATE_INTEGRATION.md - Detailed integration documentation

Files Modified

• biahub/cli/main.py - Added template CLI commands

Usage

Copy Template for New Project

cp -r biahub/templates/mantis ~/my-experiment
cd ~/my-experiment
export DATASET=my_dataset_name
python run_pipeline.py

Using Template CLI

# Initialize new project
biahub template init -t mantis -o ~/my-experiment --dataset exp_2026

# List templates
biahub template list

# Get template info
biahub template info mantis

Integration Approach

Templates are kept separate from biahub core code to:

• ✅ Preserve modularity and clear separation
• ✅ Enable easy customization by users
• ✅ Support multiple workflow variants
• ✅ Provide real-world usage examples
• ✅ Allow independent versioning

Templates orchestrate biahub commands and provide:

• Workflow logic and orchestration
• Environment management
• Error handling and logging
• Visualization tools

Source

Original repository: https://github.com/czbiohub-sf/mantis-analysis-template

• main branch → templates/mantis/
• dragonfly branch → templates/dragonfly/
• zebraphysics-mantis-pipeline branch → templates/zebraphysics-mantis-pipeline/

Documentation

• templates/README.md - Quick start guide
• MANTIS_TEMPLATE_INTEGRATION.md - Detailed integration docs
• Individual template READMEs - Workflow-specific guides

Benefits

For Users:

• Quick project initialization from proven workflows
• Best practices and configurations included
• Complete documentation
• Easy customization

For Biahub:

• Real-world usage examples
• Integration testing
• Community contribution pathway
• Flexible template ecosystem

See MANTIS_TEMPLATE_INTEGRATION.md for complete details.