Automated_BBP_Diagnostics

Software for automation of instrument for automated detection of bloodborne pathogens. Developed as a part of the UW Lutz lab. Project in press for publication.

Integrated Device Data Analysis & Control

Overview

This repository contains scripts for operating an integrated diagnostic device and performing post-processing analysis of experimental data.

The workflow includes:

1. Device control and experiment execution (motor control, thermal cycling, amplification)
2. Data parsing and preprocessing
3. Timing and system performance analysis
4. Fluorescence signal processing (FAM/TEX)
5. Detection time and SNR calculations
6. Automated plotting and export of results

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Repository Structure

Integrated Device Manuscript Final Scripts/

├── Device Amplification Processing.py # Master script to run full analysis pipeline
├── 251013_Amplification_.py # ODrive device control + experiment execution
├── 251023_Amplification_.ino # Microcontroller / firmware code

├── Data Analysis Post-Processing/
│ ├── 1_Setup.py # Load raw data and initialize environment
│ ├── 2_Data_Process.py # Clean and organize data by wells and channels
│ ├── 3_Timing.py # Extract timing events (heating, amplification)
│ ├── 4_temperature_position_graphs.py # Temperature + motion visualization
│ ├── 5_Fluorescence.py # Fluorescence processing + filtering + fitting
│ ├── 6_Liftoff_Time.py # Detection time + SNR analysis
│ ├── 7_Save.py # Save figures and export data

├── *.csv # Example output data
└── venv/ # Python virtual environment (optional)

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Workflow

Run Full Pipeline

python Device\ Amplification\ Processing.py

Or Run Step-by-Step

%run -i 1_Setup.py
%run -i 2_Data_Process.py
%run -i 3_Timing.py
%run -i 4_temperature_position_graphs.py
%run -i 5_Fluorescence.py
%run -i 6_Liftoff_Time.py
%run -i 7_Save.py

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Step Descriptions

1_Setup.py

• Select raw .txt data file via GUI
• Parses header and loads into a DataFrame
• Initializes output directories

2_Data_Process.py

• Converts timestamps to elapsed time (minutes)
• Computes well position and deviation
• Splits data into FAM and TEX channels

3_Timing.py

• Identifies key experimental events:
  • Start of run
  • Reach 50°C
  • Reach 65°C
• Computes timing intervals and exports CSV

4_temperature_position_graphs.py

• Generates plots for:
  • Temperature profiles
  • Heating behavior
  • Position tracking
  • System status

5_Fluorescence.py

• Processes fluorescence signals:
  • Raw and filtered FAM/TEX
  • Outlier removal
  • Signal smoothing
• Fits amplification curves (4-parameter logistic model)

6_Liftoff_Time.py

• Computes detection time (real-time call)
• Calculates SNR metrics
• Outputs detection summary and rolling averages

7_Save.py

• Saves:
  • Figures (PNG + PDF)
  • Processed datasets
  • Fluorescence tables

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Outputs

Generated in: Output_Analysis/_/

Includes:

• Figures (PNG + PDF)
• Timing results CSV
• Fluorescence data CSV
• Detection + SNR summary
• Rolling averages

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Dependencies

Install required packages:

pip install pandas numpy matplotlib seaborn scipy tkinter openpyxl

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Notes

• Scripts rely on shared variables, so execution order matters
• Designed for interactive use (Jupyter/IPython recommended)
• Raw data must match expected column format

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Context

This codebase supports development of an integrated molecular diagnostic system combining:

• Thermal control
• Disk-based fluidics
• Optical fluorescence detection
• Automated data analysis