automorphotrack 2.0.1

Automated pipeline for mitochondrial and lysosomal detection, tracking, morphology, and colocalization analysis in microscopy images.

AutoMorphoTrack

AutoMorphoTrack is a modular image-analysis pipeline for automated detection, morphology classification, shape profiling, motility tracking, and colocalization analysis of mitochondria and lysosomes in multichannel fluorescence microscopy data.

Developed by Armin Bayati, Ph.D.

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🧬 Overview

AutoMorphoTrack processes time-lapse .tif stacks (typically two-channel: mitochondria + lysosomes) and generates publication-ready visual and quantitative outputs at every step.

Pipeline stages:

1. Detection – Organelle segmentation and outline visualization
2. Lysosomal Counting – Per-frame lysosome counts and plots
3. Morphology Classification – Elongated vs. punctate mitochondria
4. Shape Feature Extraction – Circularity, solidity, aspect ratio, orientation
5. Shape Profiling – Combined violin plots of mitochondrial and lysosomal metrics
6. Tracking – Cumulative organelle trajectories (mitochondria, lysosomes, composite)
7. Tracking Overlay – Tracks drawn on real-intensity images
8. Motility Analysis – Velocity and displacement distributions + scatter plots
9. Colocalization – Bright-blue overlap visualization with Manders and Pearson coefficients
10. Integrated Summary – Correlation matrix across all extracted metrics

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📁 Installation

pip install automorphotrack

Or clone directly:

git clone https://github.com/abayatibrain/AutoMorphoTrack.git
cd AutoMorphoTrack
pip install -e .

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🚀 Basic Usage

from automorphotrack import *

tif_path = "Composite.tif"

detect_organelles(tif_path)
count_lysosomes_per_frame(tif_path)
classify_morphology(tif_path)
analyze_shape_features(tif_path)
profile_shape_data()
track_organelles(tif_path)
track_overlay(tif_path)
analyze_motility()
analyze_colocalization(tif_path)
summarize_integrated_data()

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📦 Outputs

Step	Output Type	Example Files
Detection	PNG + MP4	Mito_Frame0.png, Mitochondria_Detection.mp4
Lysosome Count	PNG + CSV + MP4	Lyso_Count_Plot.png, Lysosome_Counts.csv
Morphology	PNG + MP4 + CSV	Morphology_Frame0_Labeled.png, Morphology_Labeled.mp4
Shape Features	PNG + CSV	Shape_Distributions.png, Mito_ShapeMetrics.csv
Shape Profiling	PNG + CSV	Shape_ViolinPlots.png, Combined_ShapeData.csv
Tracking	PNG + MP4 + CSV	Cumulative_Mito.png, Mito_Tracks.csv
Tracking Overlay	PNG + MP4	Cumulative_Composite.png, Composite_CumulativeTracks.mp4
Motility	PNG + CSV	Motility_Distributions.png, Motility_Scatter.png
Colocalization	PNG + MP4 + CSV	Colocalization_Frame0.png, Colocalization.csv
Summary	PNG + CSV	Integrated_CorrelationMatrix.png, Integrated_Merged_Data.csv

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🔧 Dependencies

• Python ≥ 3.9
• numpy, pandas, matplotlib, seaborn, opencv-python, scikit-image, scipy, tifffile

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🧩 Citation

If you use this pipeline in your work, please cite:

Bayati, A. et al. AutoMorphoTrack: Automated Organelle Tracking and Morphometric Profiling Toolkit (2025)