AutoMorphoTrack 1.0.5__tar.gz → 2.0.1__tar.gz

automorphotrack-2.0.1/MANIFEST.in

@@ -0,0 +1,3 @@
+include README.md
+include LICENSE.md
+recursive-include automorphotrack *.py

{automorphotrack-1.0.5/AutoMorphoTrack.egg-info → automorphotrack-2.0.1}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
-Name: AutoMorphoTrack
-Version: 1.0.5
-Summary: AutoMorphoTrack is an open-source Python package for automated detection, morphology classification, motility tracking, and colocalization analysis of organelles in multichannel fluorescence microscopy data.
+Name: automorphotrack
+Version: 2.0.1
+Summary: Automated pipeline for mitochondrial and lysosomal detection, tracking, morphology, and colocalization analysis in microscopy images.
 Home-page: https://github.com/abayatibrain/AMTpackage
-Author: Armin Bayati
+Author: Armin Bayati, Ph.D.
 Author-email: a.bayati.brain@gmail.com
 License: MIT
 Project-URL: Documentation, https://github.com/abayatibrain/AMTpackage
@@ -40,45 +40,42 @@ Dynamic: summary
 
 # AutoMorphoTrack
 
-**AutoMorphoTrack** is an open-source Python package for automated detection, morphology classification, shape profiling, motility tracking, and colocalization analysis of subcellular organelles in multichannel fluorescence microscopy data.  
+**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.
 
-This package represents the fully modular version of the **AutoMorphoTrack pipeline**, originally developed as a Jupyter Notebook by **Armin Bayati, Ph.D.**, and now distributed as an installable Python framework.  
-Repository: [https://github.com/abayatibrain/automorphotrack](https://github.com/abayatibrain/automorphotrack)
+Developed by **Armin Bayati, Ph.D.**
 
 ---
 
 ## 🧬 Overview
 
-AutoMorphoTrack automates quantitative analysis of time-lapse `.tif` image stacks—typically dual-channel recordings of mitochondria and lysosomes—and generates publication-ready visual and numerical outputs at every step of the analysis pipeline.
+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 enumeration and temporal profiling  
+2. **Lysosomal Counting** – Per-frame lysosome counts and plots  
 3. **Morphology Classification** – Elongated vs. punctate mitochondria  
-4. **Shape Feature Extraction** – Area, circularity, solidity, aspect ratio, orientation  
-5. **Tracking** – Cumulative organelle trajectories (mitochondria, lysosomes, composite)  
-6. **Motility Analysis** – Velocity, displacement, and trajectory-based statistics  
-7. **Colocalization** – Bright-blue overlap overlays and correlation metrics  
-8. **Integrated Summary** – Correlation matrices linking morphology, motility, and overlap  
-
-Each stage outputs high-resolution figures, videos, and CSV data tables stored in standardized subdirectories, ensuring reproducibility and compatibility with any image dataset.
+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  
 
 ---
 
-## 📦 Installation
-
-Install directly from PyPI:
+## 📁 Installation
 
 ```bash
-pip install AutoMorphoTrack
+pip install automorphotrack
 ```
 
-Or from source:
+Or clone directly:
 
 ```bash
-git clone https://github.com/abayatibrain/automorphotrack.git
-cd automorphotrack
+git clone https://github.com/abayatibrain/AutoMorphoTrack.git
+cd AutoMorphoTrack
 pip install -e .
 ```
 
@@ -95,17 +92,17 @@ 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()
 ```
 
-Each function automatically generates visual and quantitative outputs at every step.
-
 ---
 
-## 📁 Outputs
+## 📦 Outputs
 
 | Step | Output Type | Example Files |
 |------|--------------|---------------|
@@ -113,7 +110,9 @@ Each function automatically generates visual and quantitative outputs at every s
 | 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` |
@@ -129,7 +128,6 @@ Each function automatically generates visual and quantitative outputs at every s
 
 ## 🧩 Citation
 
-If you use **AutoMorphoTrack** in your research, please cite:
+If you use this pipeline in your work, please cite:
 
-> **Bayati, A. (2025)**. AutoMorphoTrack: An accessible Python framework for automated analysis of organelle morphology and motility.  
-> *GitHub Repository:* [https://github.com/abayatibrain/automorphotrack](https://github.com/abayatibrain/automorphotrack)
+> **Bayati, A. et al.** AutoMorphoTrack: Automated Organelle Tracking and Morphometric Profiling Toolkit (2025)

automorphotrack-2.0.1/README.md

@@ -0,0 +1,93 @@
+# 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.**
+
+---
+
+## 🧬 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  
+
+---
+
+## 📁 Installation
+
+```bash
+pip install automorphotrack
+```
+
+Or clone directly:
+
+```bash
+git clone https://github.com/abayatibrain/AutoMorphoTrack.git
+cd AutoMorphoTrack
+pip install -e .
+```
+
+---
+
+## 🚀 Basic Usage
+
+```python
+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()
+```
+
+---
+
+## 📦 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` |
+
+---
+
+## 🔧 Dependencies
+
+- Python ≥ 3.9  
+- numpy, pandas, matplotlib, seaborn, opencv-python, scikit-image, scipy, tifffile
+
+---
+
+## 🧩 Citation
+
+If you use this pipeline in your work, please cite:
+
+> **Bayati, A. et al.** AutoMorphoTrack: Automated Organelle Tracking and Morphometric Profiling Toolkit (2025)

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/__init__.py

@@ -33,7 +33,7 @@
 #     )
 # ============================================================
 
-__version__ = "1.0.0"
+__version__ = "2.0.1"
 __author__ = "Armin Bayati"
 
 # --- Utility Imports ---

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/colocalization.py

@@ -7,6 +7,10 @@ from skimage.filters import threshold_otsu
 from pathlib import Path
 from automorphotrack.utils import ensure_dir, save_high_dpi
 
+# Colorblind-friendly palette
+CB_MITO = "#0173B2"   # blue
+CB_LYSO = "#DE8F05"   # orange
+
 def analyze_colocalization(
     tif_path="Composite.tif",
     mito_channel=0,
@@ -93,7 +97,7 @@ def analyze_colocalization(
         "Manders_M1": m1_list,
         "Manders_M2": m2_list,
         "Pearson_r": pearson_r,
-        "Overlap_R": overlap_R,
+        "Cosine_Similarity": overlap_R,  # Renamed from Overlap_R for clarity
         "Mito_TotalIntensity": mito_sum,
         "Lyso_TotalIntensity": lyso_sum
     }).to_csv(csv_path, index=False)
@@ -112,11 +116,11 @@ def analyze_colocalization(
     # ---------- Plot metrics ----------
     plot_path = Path(out_dir) / "Colocalization_MetricsPlot.png"
     fig, ax = plt.subplots(figsize=(10, 9))
-    ax.plot(m1_list, 'r-', label='Manders M1 (mito→lyso)')
-    ax.plot(m2_list, 'g-', label='Manders M2 (lyso→mito)')
-    ax.plot(np.array(overlap_percent) / 100, 'b--', label='Overlap fraction')
-    ax.plot(pearson_r, 'k-.', label='Pearson r')
-    ax.plot(overlap_R, 'm:', label='Normalized R')
+    ax.plot(m1_list, color=CB_MITO, linestyle='-', label='Manders M1 (mito\u2192lyso)')
+    ax.plot(m2_list, color=CB_LYSO, linestyle='-', label='Manders M2 (lyso\u2192mito)')
+    ax.plot(np.array(overlap_percent) / 100, 'b--', label='Jaccard overlap fraction')
+    ax.plot(pearson_r, 'k-.', label='Pearson r (intensity)')
+    ax.plot(overlap_R, color='#CC79A7', linestyle=':', label='Cosine similarity')
     ax.set_xlabel("Frame")
     ax.set_ylabel("Coefficient / Fraction (0–1)")
     ax.set_ylim(0, 1)

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/detection.py

@@ -12,7 +12,7 @@ from automorphotrack.utils import ensure_dir, write_video, upscale_frame
 def detect_mask(frame, ch, thr_factor=0.8, min_size=3):
     """Threshold and clean a single channel."""
     img = frame[..., ch].astype(float)
-    img = (img - img.min()) / (img.ptp() + 1e-12)
+    img = (img - img.min()) / (np.ptp(img) + 1e-12)
     thr = threshold_otsu(img) * thr_factor
     mask = clear_border(binary_opening(img > thr, footprint=disk(1)))
     mask = remove_small_objects(mask, min_size)
@@ -41,7 +41,7 @@ def detect_organelles(
         mito_gray = (mito_img * 255).astype(np.uint8)
         mito_rgb = cv2.cvtColor(mito_gray, cv2.COLOR_GRAY2RGB)
         cnts, _ = cv2.findContours(mito_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
-        cv2.drawContours(mito_rgb, cnts, -1, (255, 0, 0), 1, cv2.LINE_AA)
+        cv2.drawContours(mito_rgb, cnts, -1, (1, 115, 178), 1, cv2.LINE_AA)  # CB blue
         mito_frames.append(upscale_frame(mito_rgb, upscale_factor))
 
         # ----- Lysosomes (standard detection) -----
@@ -49,7 +49,7 @@ def detect_organelles(
         lyso_gray = (lyso_img * 255).astype(np.uint8)
         lyso_rgb = cv2.cvtColor(lyso_gray, cv2.COLOR_GRAY2RGB)
         cnts, _ = cv2.findContours(lyso_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
-        cv2.drawContours(lyso_rgb, cnts, -1, (0, 255, 0), 1, cv2.LINE_AA)
+        cv2.drawContours(lyso_rgb, cnts, -1, (222, 143, 5), 1, cv2.LINE_AA)  # CB orange
         lyso_frames.append(upscale_frame(lyso_rgb, upscale_factor))
 
     # Save representative frames

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/lyso_count.py

@@ -12,7 +12,7 @@ from automorphotrack.utils import ensure_dir, write_video, upscale_frame
 def detect_mask(frame, ch, thr_factor=0.8, min_size=2):
     """Detect lysosomes in a single channel frame."""
     img = frame[..., ch].astype(float)
-    img = (img - img.min()) / (img.ptp() + 1e-12)
+    img = (img - img.min()) / (np.ptp(img) + 1e-12)
     thr = threshold_otsu(img) * thr_factor
     mask = clear_border(binary_opening(img > thr, footprint=disk(1)))
     mask = remove_small_objects(mask, min_size)
@@ -42,15 +42,15 @@ def count_lysosomes_per_frame(
 
         lyso_gray = (lyso_img * 255).astype(np.uint8)
         lyso_rgb = cv2.cvtColor(lyso_gray, cv2.COLOR_GRAY2RGB)
-        cv2.drawContours(lyso_rgb, cnts, -1, (0, 255, 0), 1, cv2.LINE_AA)
+        cv2.drawContours(lyso_rgb, cnts, -1, (222, 143, 5), 1, cv2.LINE_AA)  # CB orange
 
-        # Add small green numbers at each lysosome position
+        # Add small orange numbers at each lysosome position
         for i, c in enumerate(cnts):
             M = cv2.moments(c)
             if M["m00"] != 0:
                 cx, cy = int(M["m10"] / M["m00"]), int(M["m01"] / M["m00"])
                 cv2.putText(lyso_rgb, str(i + 1), (cx, cy),
-                            cv2.FONT_HERSHEY_SIMPLEX, 0.35, (0, 255, 0), 1, cv2.LINE_AA)
+                            cv2.FONT_HERSHEY_SIMPLEX, 0.35, (222, 143, 5), 1, cv2.LINE_AA)
 
         # Add total count label in white (small font)
         cv2.putText(lyso_rgb, f"Count: {lyso_count}", (10, 18),
@@ -72,7 +72,7 @@ def count_lysosomes_per_frame(
 
     # Plot counts over frames
     plt.figure(figsize=(6, 4))
-    plt.plot(df["Frame"], df["Lysosome_Count"], "-o", color="green")
+    plt.plot(df["Frame"], df["Lysosome_Count"], "-o", color="#DE8F05")
     plt.xlabel("Frame")
     plt.ylabel("Lysosome Count")
     plt.title("Lysosome Count per Frame")

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/morphology.py

@@ -13,7 +13,7 @@ from automorphotrack.utils import ensure_dir, upscale_frame, save_high_dpi
 def detect_mask(frame, ch, thr_factor=0.8, min_size=10):
     """Threshold a channel to obtain clean mitochondrial mask."""
     img = frame[..., ch].astype(float)
-    img = (img - img.min()) / (img.ptp() + 1e-12)
+    img = (img - img.min()) / (np.ptp(img) + 1e-12)
     thr = threshold_otsu(img) * thr_factor
     mask = clear_border(binary_opening(img > thr, footprint=disk(1)))
     mask = remove_small_objects(mask, min_size)

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/motility.py

@@ -6,6 +6,10 @@ import pandas as pd, numpy as np, matplotlib.pyplot as plt, seaborn as sns
 from pathlib import Path
 from automorphotrack.utils import ensure_dir, save_high_dpi
 
+# Colorblind-friendly palette (Okabe-Ito inspired)
+CB_MITO = "#0173B2"   # blue
+CB_LYSO = "#DE8F05"   # orange
+
 def analyze_motility(
     mito_tracks_path="Tracking_Outputs/Mito_Tracks.csv",
     lyso_tracks_path="Tracking_Outputs/Lyso_Tracks.csv",
@@ -71,16 +75,19 @@ def analyze_motility(
 
     # ---------- Distribution Plots ----------
     fig, axes = plt.subplots(1, 2, figsize=(20, 8))
-    sns.kdeplot(mito_summary["Mean_Velocity"], color="red", fill=True, ax=axes[0], label="Mitochondria")
-    sns.kdeplot(lyso_summary["Mean_Velocity"], color="green", fill=True, alpha=0.4, ax=axes[0], label="Lysosomes")
+    # clip=(0, None) prevents KDE from extending into physically invalid negative values
+    sns.kdeplot(mito_summary["Mean_Velocity"], color=CB_MITO, fill=True, ax=axes[0], label="Mitochondria", clip=(0, None))
+    sns.kdeplot(lyso_summary["Mean_Velocity"], color=CB_LYSO, fill=True, alpha=0.4, ax=axes[0], label="Lysosomes", clip=(0, None))
     axes[0].set_title("Mean Velocity Distribution")
     axes[0].set_xlabel("Velocity (px/frame)")
+    axes[0].set_xlim(left=0)
     axes[0].legend()
 
-    sns.kdeplot(mito_summary["Total_Displacement"], color="red", fill=True, ax=axes[1], label="Mitochondria")
-    sns.kdeplot(lyso_summary["Total_Displacement"], color="green", fill=True, alpha=0.4, ax=axes[1], label="Lysosomes")
+    sns.kdeplot(mito_summary["Total_Displacement"], color=CB_MITO, fill=True, ax=axes[1], label="Mitochondria", clip=(0, None))
+    sns.kdeplot(lyso_summary["Total_Displacement"], color=CB_LYSO, fill=True, alpha=0.4, ax=axes[1], label="Lysosomes", clip=(0, None))
     axes[1].set_title("Total Displacement Distribution")
     axes[1].set_xlabel("Displacement (px)")
+    axes[1].set_xlim(left=0)
     axes[1].legend()
 
     plt.tight_layout()
@@ -89,9 +96,9 @@ def analyze_motility(
     # ---------- Scatter Plot ----------
     fig, ax = plt.subplots(figsize=(12, 10))
     sns.scatterplot(data=mito_summary, x="Total_Displacement", y="Mean_Velocity",
-                    color="red", s=30, label="Mitochondria")
+                    color=CB_MITO, s=30, label="Mitochondria")
     sns.scatterplot(data=lyso_summary, x="Total_Displacement", y="Mean_Velocity",
-                    color="green", s=30, alpha=0.6, label="Lysosomes")
+                    color=CB_LYSO, s=30, alpha=0.6, label="Lysosomes")
     ax.set_xlabel("Total Displacement (px)")
     ax.set_ylabel("Mean Velocity (px/frame)")
     ax.set_title("Motility Scatter Plot")

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/shape_features.py

@@ -10,10 +10,14 @@ from skimage.segmentation import clear_border
 from pathlib import Path
 from automorphotrack.utils import ensure_dir, save_high_dpi, upscale_frame
 
+# Colorblind-friendly palette (Okabe-Ito inspired)
+CB_MITO = "#0173B2"   # blue
+CB_LYSO = "#DE8F05"   # orange
+
 def detect_mask(frame, ch, min_size=3, thr_factor=0.8):
     """Threshold and clean a single channel."""
     img = frame[..., ch].astype(float)
-    img = (img - img.min()) / (img.ptp() + 1e-12)
+    img = (img - img.min()) / (np.ptp(img) + 1e-12)
     thr = threshold_otsu(img) * thr_factor
     mask = clear_border(binary_opening(img > thr, footprint=disk(1)))
     mask = remove_small_objects(mask, min_size)
@@ -41,7 +45,11 @@ def analyze_shape_features(
         for p in regionprops(lbl_m):
             if p.area < 5:
                 continue
-            circ = (4 * np.pi * p.area) / (p.perimeter ** 2 + 1e-9)
+            # Use perimeter_crofton for more accurate continuous perimeter estimate
+            # to avoid circularity > 1 due to discrete pixel-boundary underestimation
+            perim = getattr(p, 'perimeter_crofton', p.perimeter)
+            circ = (4 * np.pi * p.area) / (perim ** 2 + 1e-9)
+            circ = min(circ, 1.0)  # Clamp to [0, 1] for physical validity
             aspect = p.major_axis_length / (p.minor_axis_length + 1e-9)
             mito_records.append({
                 "Frame": f,
@@ -59,7 +67,9 @@ def analyze_shape_features(
         for p in regionprops(lbl_l):
             if p.area < 5:
                 continue
-            circ = (4 * np.pi * p.area) / (p.perimeter ** 2 + 1e-9)
+            perim = getattr(p, 'perimeter_crofton', p.perimeter)
+            circ = (4 * np.pi * p.area) / (perim ** 2 + 1e-9)
+            circ = min(circ, 1.0)  # Clamp to [0, 1] for physical validity
             aspect = p.major_axis_length / (p.minor_axis_length + 1e-9)
             lyso_records.append({
                 "Frame": f,
@@ -82,14 +92,15 @@ def analyze_shape_features(
 
     # ---------- KDE Distribution Plots ----------
     fig, axes = plt.subplots(1, 2, figsize=(20, 8))
-    sns.kdeplot(mito_df["Circularity"], ax=axes[0], color="red", fill=True, alpha=0.5, label="Mito")
-    sns.kdeplot(lyso_df["Circularity"], ax=axes[0], color="green", fill=True, alpha=0.4, label="Lyso")
+    sns.kdeplot(mito_df["Circularity"], ax=axes[0], color=CB_MITO, fill=True, alpha=0.5, label="Mito", clip=(0, 1))
+    sns.kdeplot(lyso_df["Circularity"], ax=axes[0], color=CB_LYSO, fill=True, alpha=0.4, label="Lyso", clip=(0, 1))
     axes[0].set_title("Circularity Distribution")
-    axes[0].set_xlabel("Circularity (4πA/P²)")
+    axes[0].set_xlabel("Circularity (4\u03C0A/P\u00B2)")
+    axes[0].set_xlim(0, 1)
     axes[0].legend(frameon=False)
 
-    sns.kdeplot(mito_df["Solidity"], ax=axes[1], color="red", fill=True, alpha=0.5, label="Mito")
-    sns.kdeplot(lyso_df["Solidity"], ax=axes[1], color="green", fill=True, alpha=0.4, label="Lyso")
+    sns.kdeplot(mito_df["Solidity"], ax=axes[1], color=CB_MITO, fill=True, alpha=0.5, label="Mito", clip=(0, 1))
+    sns.kdeplot(lyso_df["Solidity"], ax=axes[1], color=CB_LYSO, fill=True, alpha=0.4, label="Lyso", clip=(0, 1))
     axes[1].set_title("Solidity Distribution")
     axes[1].set_xlabel("Solidity")
     axes[1].legend(frameon=False)

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/shape_profiling.py

@@ -34,7 +34,7 @@ def profile_shape_data(
             data=combined_df,
             x="Type",
             y=metric,
-            palette={"Mitochondria": "red", "Lysosomes": "green"},
+            palette={"Mitochondria": "#0173B2", "Lysosomes": "#DE8F05"},
             cut=0,
             inner="quartile",
             ax=ax

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/summary.py

@@ -3,6 +3,7 @@
 # ============================================================
 
 import pandas as pd, numpy as np, matplotlib.pyplot as plt, seaborn as sns
+from scipy.stats import spearmanr
 from pathlib import Path
 from automorphotrack.utils import ensure_dir
 
@@ -44,10 +45,18 @@ def summarize_integrated_data(
     )
     print(f"Merged dataset dimensions: {merged.shape[0]} rows × {merged.shape[1]} columns")
 
-    # ---------- Correlation computation ----------
+    # ---------- Correlation computation (Spearman rank) ----------
+    # Spearman is preferred over Pearson for biological morphometric data
+    # because many relationships are non-linear and distributions are non-normal
     numeric_cols = merged.select_dtypes(include=[np.number])
-    corr = numeric_cols.corr().round(2)
-    print("Correlation matrix computed")
+    cols = numeric_cols.columns
+    rho_matrix = np.zeros((len(cols), len(cols)))
+    for i, c1 in enumerate(cols):
+        for j, c2 in enumerate(cols):
+            rho, _ = spearmanr(numeric_cols[c1], numeric_cols[c2])
+            rho_matrix[i, j] = rho
+    corr = pd.DataFrame(rho_matrix, index=cols, columns=cols).round(2)
+    print("Spearman correlation matrix computed")
 
     # ---------- Save results ----------
     out_dir = Path(out_dir)
@@ -61,7 +70,7 @@ def summarize_integrated_data(
     # ---------- Plot correlation heatmap ----------
     fig, ax = plt.subplots(figsize=(28, 20))
     sns.heatmap(corr, annot=True, fmt=".2f", cmap="coolwarm", square=True)
-    ax.set_title("Integrated Correlation Matrix – Shape, Motility, Colocalization", fontsize=14)
+    ax.set_title("Integrated Spearman Correlation Matrix \u2013 Shape, Motility, Colocalization", fontsize=14)
     plt.tight_layout()
     heatmap_path = out_dir / "Integrated_CorrelationMatrix.png"
     plt.savefig(heatmap_path, dpi=300)

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/tracking.py

@@ -98,11 +98,11 @@ def track_organelles(
         mito_frame, lyso_frame, comp_frame = frame_rgb.copy(), frame_rgb.copy(), frame_rgb.copy()
 
         for p1, p2 in mito_paths:
-            cv2.line(mito_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (255, 0, 0), 1)
-            cv2.line(comp_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (255, 0, 0), 1)
+            cv2.line(mito_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (1, 115, 178), 1)
+            cv2.line(comp_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (1, 115, 178), 1)
         for p1, p2 in lyso_paths:
-            cv2.line(lyso_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (0, 255, 0), 1)
-            cv2.line(comp_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (0, 255, 0), 1)
+            cv2.line(lyso_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (222, 143, 5), 1)
+            cv2.line(comp_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])), (222, 143, 5), 1)
 
         mito_frames.append(upscale_frame(mito_frame))
         lyso_frames.append(upscale_frame(lyso_frame))

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/automorphotrack/tracking_overlay.py

@@ -95,14 +95,14 @@ def track_overlay(
 
         for p1, p2 in mito_paths:
             cv2.line(mito_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])),
-                     (255, 0, 0), line_thickness, cv2.LINE_AA)
+                     (1, 115, 178), line_thickness, cv2.LINE_AA)
             cv2.line(comp_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])),
-                     (255, 0, 0), line_thickness, cv2.LINE_AA)
+                     (1, 115, 178), line_thickness, cv2.LINE_AA)
         for p1, p2 in lyso_paths:
             cv2.line(lyso_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])),
-                     (0, 255, 0), line_thickness, cv2.LINE_AA)
+                     (222, 143, 5), line_thickness, cv2.LINE_AA)
             cv2.line(comp_frame, tuple(np.int32(p1[::-1])), tuple(np.int32(p2[::-1])),
-                     (0, 255, 0), line_thickness, cv2.LINE_AA)
+                     (222, 143, 5), line_thickness, cv2.LINE_AA)
 
         mito_frames.append(upscale_frame(mito_frame))
         lyso_frames.append(upscale_frame(lyso_frame))

{automorphotrack-1.0.5 → automorphotrack-2.0.1/automorphotrack.egg-info}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
-Name: AutoMorphoTrack
-Version: 1.0.5
-Summary: AutoMorphoTrack is an open-source Python package for automated detection, morphology classification, motility tracking, and colocalization analysis of organelles in multichannel fluorescence microscopy data.
+Name: automorphotrack
+Version: 2.0.1
+Summary: Automated pipeline for mitochondrial and lysosomal detection, tracking, morphology, and colocalization analysis in microscopy images.
 Home-page: https://github.com/abayatibrain/AMTpackage
-Author: Armin Bayati
+Author: Armin Bayati, Ph.D.
 Author-email: a.bayati.brain@gmail.com
 License: MIT
 Project-URL: Documentation, https://github.com/abayatibrain/AMTpackage
@@ -40,45 +40,42 @@ Dynamic: summary
 
 # AutoMorphoTrack
 
-**AutoMorphoTrack** is an open-source Python package for automated detection, morphology classification, shape profiling, motility tracking, and colocalization analysis of subcellular organelles in multichannel fluorescence microscopy data.  
+**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.
 
-This package represents the fully modular version of the **AutoMorphoTrack pipeline**, originally developed as a Jupyter Notebook by **Armin Bayati, Ph.D.**, and now distributed as an installable Python framework.  
-Repository: [https://github.com/abayatibrain/automorphotrack](https://github.com/abayatibrain/automorphotrack)
+Developed by **Armin Bayati, Ph.D.**
 
 ---
 
 ## 🧬 Overview
 
-AutoMorphoTrack automates quantitative analysis of time-lapse `.tif` image stacks—typically dual-channel recordings of mitochondria and lysosomes—and generates publication-ready visual and numerical outputs at every step of the analysis pipeline.
+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 enumeration and temporal profiling  
+2. **Lysosomal Counting** – Per-frame lysosome counts and plots  
 3. **Morphology Classification** – Elongated vs. punctate mitochondria  
-4. **Shape Feature Extraction** – Area, circularity, solidity, aspect ratio, orientation  
-5. **Tracking** – Cumulative organelle trajectories (mitochondria, lysosomes, composite)  
-6. **Motility Analysis** – Velocity, displacement, and trajectory-based statistics  
-7. **Colocalization** – Bright-blue overlap overlays and correlation metrics  
-8. **Integrated Summary** – Correlation matrices linking morphology, motility, and overlap  
-
-Each stage outputs high-resolution figures, videos, and CSV data tables stored in standardized subdirectories, ensuring reproducibility and compatibility with any image dataset.
+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  
 
 ---
 
-## 📦 Installation
-
-Install directly from PyPI:
+## 📁 Installation
 
 ```bash
-pip install AutoMorphoTrack
+pip install automorphotrack
 ```
 
-Or from source:
+Or clone directly:
 
 ```bash
-git clone https://github.com/abayatibrain/automorphotrack.git
-cd automorphotrack
+git clone https://github.com/abayatibrain/AutoMorphoTrack.git
+cd AutoMorphoTrack
 pip install -e .
 ```
 
@@ -95,17 +92,17 @@ 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()
 ```
 
-Each function automatically generates visual and quantitative outputs at every step.
-
 ---
 
-## 📁 Outputs
+## 📦 Outputs
 
 | Step | Output Type | Example Files |
 |------|--------------|---------------|
@@ -113,7 +110,9 @@ Each function automatically generates visual and quantitative outputs at every s
 | 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` |
@@ -129,7 +128,6 @@ Each function automatically generates visual and quantitative outputs at every s
 
 ## 🧩 Citation
 
-If you use **AutoMorphoTrack** in your research, please cite:
+If you use this pipeline in your work, please cite:
 
-> **Bayati, A. (2025)**. AutoMorphoTrack: An accessible Python framework for automated analysis of organelle morphology and motility.  
-> *GitHub Repository:* [https://github.com/abayatibrain/automorphotrack](https://github.com/abayatibrain/automorphotrack)
+> **Bayati, A. et al.** AutoMorphoTrack: Automated Organelle Tracking and Morphometric Profiling Toolkit (2025)

automorphotrack-2.0.1/automorphotrack.egg-info/SOURCES.txt

@@ -0,0 +1,34 @@
+LICENSE.md
+MANIFEST.in
+README.md
+pyproject.toml
+setup.py
+automorphotrack/.___init__.py
+automorphotrack/._colocalization.py
+automorphotrack/._detection.py
+automorphotrack/._lyso_count.py
+automorphotrack/._morphology.py
+automorphotrack/._motility.py
+automorphotrack/._shape_features.py
+automorphotrack/._shape_profiling.py
+automorphotrack/._summary.py
+automorphotrack/._tracking.py
+automorphotrack/._tracking_overlay.py
+automorphotrack/._utils.py
+automorphotrack/__init__.py
+automorphotrack/colocalization.py
+automorphotrack/detection.py
+automorphotrack/lyso_count.py
+automorphotrack/morphology.py
+automorphotrack/motility.py
+automorphotrack/shape_features.py
+automorphotrack/shape_profiling.py
+automorphotrack/summary.py
+automorphotrack/tracking.py
+automorphotrack/tracking_overlay.py
+automorphotrack/utils.py
+automorphotrack.egg-info/PKG-INFO
+automorphotrack.egg-info/SOURCES.txt
+automorphotrack.egg-info/dependency_links.txt
+automorphotrack.egg-info/requires.txt
+automorphotrack.egg-info/top_level.txt

automorphotrack-2.0.1/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"

{automorphotrack-1.0.5 → automorphotrack-2.0.1}/setup.py

@@ -1,19 +1,19 @@
 from setuptools import setup, find_packages
+import os
 
-# Read the README file for the long description
-with open("README.md", "r", encoding="utf-8") as fh:
-    long_description = fh.read()
+# Read README file (handle missing file gracefully for pip install from sdist)
+long_description = ""
+readme_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "README.md")
+if os.path.exists(readme_path):
+    with open(readme_path, "r", encoding="utf-8") as fh:
+        long_description = fh.read()
 
 setup(
-    name="AutoMorphoTrack",
-    version="1.0.5",
-    author="Armin Bayati",
+    name="automorphotrack",
+    version="2.0.1",
+    author="Armin Bayati, Ph.D.",
     author_email="a.bayati.brain@gmail.com",
-    description=(
-        "AutoMorphoTrack is an open-source Python package for automated detection, "
-        "morphology classification, motility tracking, and colocalization analysis "
-        "of organelles in multichannel fluorescence microscopy data."
-    ),
+    description="Automated pipeline for mitochondrial and lysosomal detection, tracking, morphology, and colocalization analysis in microscopy images.",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/abayatibrain/AMTpackage",

automorphotrack-1.0.5/AutoMorphoTrack.egg-info/SOURCES.txt

@@ -1,21 +0,0 @@
-LICENSE.md
-MANIFEST.in
-README.md
-setup.py
-AutoMorphoTrack.egg-info/PKG-INFO
-AutoMorphoTrack.egg-info/SOURCES.txt
-AutoMorphoTrack.egg-info/dependency_links.txt
-AutoMorphoTrack.egg-info/requires.txt
-AutoMorphoTrack.egg-info/top_level.txt
-automorphotrack/__init__.py
-automorphotrack/colocalization.py
-automorphotrack/detection.py
-automorphotrack/lyso_count.py
-automorphotrack/morphology.py
-automorphotrack/motility.py
-automorphotrack/shape_features.py
-automorphotrack/shape_profiling.py
-automorphotrack/summary.py
-automorphotrack/tracking.py
-automorphotrack/tracking_overlay.py
-automorphotrack/utils.py

automorphotrack-1.0.5/MANIFEST.in

@@ -1,19 +0,0 @@
-# Include documentation and license files
-include README.md
-include LICENSE
-include requirements.txt
-
-# Include all Python source files
-recursive-include automorphotrack *.py
-
-# Include any additional data files (if present)
-recursive-include automorphotrack *.csv
-recursive-include automorphotrack *.txt
-recursive-include automorphotrack *.ipynb
-recursive-include automorphotrack *.png
-recursive-include automorphotrack *.jpg
-recursive-include automorphotrack *.tif
-recursive-include automorphotrack *.json
-
-# Exclude unnecessary system or cache files
-global-exclude __pycache__ *.py[cod] .DS_Store

automorphotrack-1.0.5/README.md

@@ -1,95 +0,0 @@
-# AutoMorphoTrack
-
-**AutoMorphoTrack** is an open-source Python package for automated detection, morphology classification, shape profiling, motility tracking, and colocalization analysis of subcellular organelles in multichannel fluorescence microscopy data.  
-
-This package represents the fully modular version of the **AutoMorphoTrack pipeline**, originally developed as a Jupyter Notebook by **Armin Bayati, Ph.D.**, and now distributed as an installable Python framework.  
-Repository: [https://github.com/abayatibrain/automorphotrack](https://github.com/abayatibrain/automorphotrack)
-
----
-
-## 🧬 Overview
-
-AutoMorphoTrack automates quantitative analysis of time-lapse `.tif` image stacks—typically dual-channel recordings of mitochondria and lysosomes—and generates publication-ready visual and numerical outputs at every step of the analysis pipeline.
-
-**Pipeline stages:**
-
-1. **Detection** – Organelle segmentation and outline visualization  
-2. **Lysosomal Counting** – Per-frame lysosome enumeration and temporal profiling  
-3. **Morphology Classification** – Elongated vs. punctate mitochondria  
-4. **Shape Feature Extraction** – Area, circularity, solidity, aspect ratio, orientation  
-5. **Tracking** – Cumulative organelle trajectories (mitochondria, lysosomes, composite)  
-6. **Motility Analysis** – Velocity, displacement, and trajectory-based statistics  
-7. **Colocalization** – Bright-blue overlap overlays and correlation metrics  
-8. **Integrated Summary** – Correlation matrices linking morphology, motility, and overlap  
-
-Each stage outputs high-resolution figures, videos, and CSV data tables stored in standardized subdirectories, ensuring reproducibility and compatibility with any image dataset.
-
----
-
-## 📦 Installation
-
-Install directly from PyPI:
-
-```bash
-pip install AutoMorphoTrack
-```
-
-Or from source:
-
-```bash
-git clone https://github.com/abayatibrain/automorphotrack.git
-cd automorphotrack
-pip install -e .
-```
-
----
-
-## 🚀 Basic Usage
-
-```python
-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)
-track_organelles(tif_path)
-analyze_motility()
-analyze_colocalization(tif_path)
-summarize_integrated_data()
-```
-
-Each function automatically generates visual and quantitative outputs at every step.
-
----
-
-## 📁 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` |
-| Tracking | PNG + MP4 + CSV | `Cumulative_Mito.png`, `Mito_Tracks.csv` |
-| 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` |
-
----
-
-## 🔧 Dependencies
-
-- Python ≥ 3.9  
-- numpy, pandas, matplotlib, seaborn, opencv-python, scikit-image, scipy, tifffile
-
----
-
-## 🧩 Citation
-
-If you use **AutoMorphoTrack** in your research, please cite:
-
-> **Bayati, A. (2025)**. AutoMorphoTrack: An accessible Python framework for automated analysis of organelle morphology and motility.  
-> *GitHub Repository:* [https://github.com/abayatibrain/automorphotrack](https://github.com/abayatibrain/automorphotrack)