Echo Transfer Processor for XChem Echo

A Notebook for generating Echo liquid handler transfer files.

Project Structure

├── Echo_Transfer_Processor.ipynb       # Main processing notebook
├── sample-prep-file.csv  # Example sample preparation data
├── README.md                           # This file

Input Data Format

The input CSV file should contain the following columns:

Column	Description
source-plate-ID	Unique identifier for the source plate
source-well	Well position in source plate (e.g., A05, B12)
sample-ID	Sample batch identifier
transfer-volume(nL)	Transfer volume in nanoliters

Output Format

Echo Transfer Files

Each generated transfer file contains:

Column	Description
PlateBatch	Destination plate name (format: Zika-NS2B-NS3_creoptix_p##)
SrcWell	Normalized source well position
Destination well	Sequential destination well (A1, B1, C1, etc.)
XferVol	Transfer volume in nanoliters

Creoptix Platemap Files (Optional)

When enabled, generates platemap files for each destination plate with:

Column	Description
Pos	Well position (A1-P24 for 384-well plate)
Designation	Sample ID for the well
Concentration	Empty (for user input)
MW	Empty (for user input)
Volume	Empty (for user input)

Usage

Prerequisites

import pandas as pd
import re
from pathlib import Path

Running the Processor

1. Prepare Input Data: Ensure your sample preparation data is in CSV format with the required columns
2. Configure Settings: Update the configuration variables in the notebook:

   PLATENAME = "Zika-NS2B-NS3"
   PLATETYPE = "creoptix"
   INPUT_FILE = "sample-prep-file.csv"
   OUTPUT_DIR = "transfer-files"
   GENERATE_CREOPTIX_FILES = True  # Set to False to skip Creoptix files

3. Execute Notebook: Run all cells in Echo_Transfer_Processor.ipynb
4. Review Outputs: Check the transfer-files/ directory for generated files

Configuration Options

• PLATENAME: Base name for destination plates
• PLATETYPE: Plate type identifier (e.g., "creoptix")
• INPUT_FILE: Path to input CSV file
• OUTPUT_DIR: Directory for output files
• GENERATE_CREOPTIX_FILES: True to generate Creoptix platemap files, False to skip

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Last updated: February 2026