OTF-Tomography

On-the-Fly Cryo-Electron Tomography Automation

A Python-based graphical interface for automating cryo-electron tomography (cryo-ET) data acquisition and processing workflows. Developed at Harvard Medical School to streamline multi-stage refinement pipelines for structural biology research.

Overview

Cryo-ET generates nanometer-resolution 3D reconstructions of biological specimens but requires complex multi-stage refinement including drift correction, motion correction, and tilt-series alignment. This GUI automates key steps in the workflow:

• Microscope configuration — Set acquisition parameters
• Motion correction — Automated drift correction for tilt series
• Tilt-series alignment — Integration with IMOD/AreTomo
• Particle picking — crYOLO integration for automated detection
• RELION preprocessing — Prepare data for subtomogram averaging

Features

• Real-time monitoring of data acquisition
• Automated pipeline execution with configurable parameters
• Integration with standard cryo-ET software (RELION, crYOLO, IMOD)
• Batch processing for high-throughput data collection
• Logging and progress tracking

Installation

Prerequisites

• Python ≥ 3.8
• RELION (for subtomogram averaging)
• IMOD or AreTomo (for alignment)

Setup

git clone https://github.com/abdullah-al-bashit/OTF_tomography.git
cd OTF_tomography

# Install Python dependencies
pip install numpy scipy tkinter

# Ensure external tools are in PATH
which relion_refine  # RELION
which cryolo_predict.py  # crYOLO

Usage

Launch GUI

python OTF-tomo.py

Pipeline Components

Module	Description
OTF-tomo.py	Main GUI application
backend_master.py	Pipeline orchestration and job management
alignment.py	Tilt-series alignment routines
prep_functions.py	Data preprocessing utilities
run_cryolo.py	crYOLO particle picking integration
rln_helpers.py	RELION helper functions
transfer_data.py	Data transfer and organization
check_run_pipeline.py	Pipeline status monitoring

Configuration

Configure paths and parameters in the GUI or edit the configuration section in backend_master.py:

# Example configuration
DATA_DIR = "/path/to/raw/data"
OUTPUT_DIR = "/path/to/processed"
RELION_PATH = "/software/relion/bin"

Project Structure

OTF_tomography/
├── OTF-tomo.py           # Main GUI application
├── OTF-tomo.png          # GUI screenshot
├── backend_master.py     # Pipeline orchestration
├── alignment.py          # Alignment routines
├── prep_functions.py     # Preprocessing utilities
├── run_cryolo.py         # crYOLO integration
├── rln_helpers.py        # RELION helpers
├── transfer_data.py      # Data transfer
├── check_run_pipeline.py # Pipeline monitoring
├── test.py               # Test suite
├── program_commands.log  # Command logging
└── README.md

Users

This tool has been used for cryo-ET data collection and structure determination by researchers at:

• Boston Children's Hospital
• Dana-Farber Cancer Institute
• Massachusetts General Hospital
• Harvard Medical School

Author

Abdullah Al Bashit, PhD
Developed as a Visiting Researcher at Harvard Medical School

License

This project is licensed under the MIT License - see LICENSE for details.

Acknowledgments

• Harvard Medical School Cryo-ET Facility
• Boston-area structural biology community