Array Print

A Python package for generating optimized printing inputs for Scienion liquid-handling robots.

Overview

Takes a .csv library file and generates Scienion-compatible .fld files that optimize sample placement for arrayed microfluidics experiments (e.g. MITOMI). Includes visualization and quality control metrics.

Installation

Install from source

# Clone the repository
git clone https://github.com/micaholivas/Array-Print.git
cd Array-Print

# Install the package
pip install -e .

# Or install with Jupyter notebook support
pip install -e ".[jupyter]"

Requirements

• Python ≥3.8
• Core dependencies: numpy, pandas, matplotlib, seaborn
• Optional: Jupyter notebook support

Package Structure

array_print/
├── __init__.py     # Main package with exported functions
├── utils.py        # Core utility functions (array generation, file I/O)
└── viz.py          # Visualization functions (plots, heatmaps)

Usage

In Python/Jupyter

import array_print as ap
import pandas as pd

# Load your library data
library_df = pd.read_csv('your_library.csv')

# Create project directory
export_dir = ap.create_project_directory('my-project')

# Generate print array
print_array = ap.generate_print_array(
    library_df=library_df,
    columns=32, rows=56,
    using_blocked_device=True,
    n_blocks=4
)

# Generate visualizations and metrics
ap.plot_mutant_frequency(print_array, export_dir)
metrics = ap.get_print_metrics(print_array)
ap.print_metrics_summary(metrics)

# Export FLD file
ap.write_fld('my-project', print_array, 32, 56, export_dir)

Using the Template Notebook

1. Open template.ipynb
2. Configure project settings (file paths, device parameters)
3. Set input CSV path with required columns: Plate, Well, Name, Rank, Block
4. Run all cells to generate complete analysis

Input Format

Your CSV file should contain:

• Plate: Plate number (int)
• Well: Well position (e.g., 'A1', 'B5')
• Name: Variant/mutant name
• Rank: Priority ranking for placement
• Block: Block assignment for blocked devices

Output

Results saved to ~/my-prints/[project-name]/ containing:

• Timestamped .fld print file for Scienion robots
• Frequency and position visualization plots
• Print metrics summary and analysis

Available Functions

Core Functions

• generate_print_array() - Create optimized array layout
• get_print_metrics() - Calculate array statistics
• create_project_directory() - Set up output directories
• write_fld() - Export Scienion-compatible files

Visualization Functions

• plot_mutant_frequency() - Show variant distribution
• plot_mutant_position() - Highlight specific variants
• plot_array_heatmap() - Array occupancy visualization
• plot_plate_layouts() - 96/384-well plate layouts

Utility Functions

• get_96_to_384() - Convert plate formats
• modify_array_column() - Array manipulation tools