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MiHCSMe-py#

A Python package for handling MIHCSME (Minimum Information about a High Content Screening Microscopy Experiment) metadata from Excel spreadsheets to OMERO annotations and back.

Features#

  • 📊 Parse MIHCSME Excel files into validated Pydantic models
  • 🔄 Bidirectional conversion between Excel, Pydantic, and OMERO formats
  • ✅ Built-in validation with helpful error messages
  • 🚀 Modern CLI with rich terminal output
  • 🐍 Type-safe with full type hints
  • 📦 Ready for PyPI distribution

Installation#

Core Package#

Install the minimal package for use in Python scripts or OMERO.scripts:

pip install mihcsme-py

With CLI Tools#

For interactive command-line use:

pip install mihcsme-py[cli]

Development Installation#

For contributors:

git clone <repository-url>
cd mihcsme_py
source .venv/bin/activate dev

Quick Start#

Parse Excel to JSON#

from mihcsme_py import parse_excel_to_model

# Parse Excel file
metadata = parse_excel_to_model("metadata.xlsx")

# Save as JSON
with open("metadata.json", "w") as f:
    f.write(metadata.model_dump_json(indent=2))

Upload to OMERO#

import ezomero
from mihcsme_py import parse_excel_to_model, upload_metadata_to_omero

# Parse metadata
metadata = parse_excel_to_model("metadata.xlsx")

# Connect to OMERO
conn = ezomero.connect(
    host="omero.example.com",
    user="myuser",
    password="mypassword"
)

# Upload to screen
result = upload_metadata_to_omero(
    conn=conn,
    metadata=metadata,
    target_type="Screen",
    target_id=123
)

print(f"Uploaded: {result['wells_succeeded']} wells")
conn.close()

CLI Usage#

# Parse Excel to JSON
mihcsme parse metadata.xlsx --output metadata.json

# Upload to OMERO
mihcsme upload metadata.xlsx \
    --screen-id 123 \
    --host omero.example.com \
    --user myuser

# Convert JSON to Excel
mihcsme to-excel metadata.json --output metadata.xlsx

Data Flow#

Excel (.xlsx) ←→ Pydantic Model ←→ JSON (.json)
                       ↓
                  OMERO Server

Supported workflows:

  1. Excel → JSON: Parse and store metadata in version control
  2. JSON → Excel: Generate editable templates
  3. Excel → OMERO: Upload metadata annotations
  4. JSON → OMERO: Upload from stored metadata

Architecture#

The package provides four main components:

  • models.py: Pydantic models for MIHCSME metadata
  • parser.py: Excel → Pydantic conversion
  • writer.py: Pydantic → Excel conversion
  • uploader.py: Pydantic → OMERO upload
  • cli.py: Command-line interface (optional, requires [cli] install)