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<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/demo.gif" alt="MELAGE Demo" width="400"/><br>
<h1 align="center">🧠🩻 MELAGE: Medical Imaging Software</h1>
<p align="center">
<em>Machine learning & analysis for next-generation neuroimaging and medical imaging research</em>
</p>
</p>
MELAGE is an open-source **medical imaging software** designed for analysis, segmentation, and visualization of multimodal datasets.
It combines classical medical image processing with state-of-the-art deep learning support, making it useful for both researchers and practitioners.
## ✨ Features
- 🧠 **Medical Image Preprocessing**: resampling, denoising, and filtering for various modalities (MRI, CT, Ultrasound, etc.).
- 🎯 **Segmentation and Labeling**: Region-based segmentation and anatomical labeling with support for standard medical formats.
- 🖼️ **Visualization**: Interactive 2D/3D visualization of images, segmentations, and anatomical structures.
- 🔗 **Deep Learning Integration (Optional)**: Seamless use of PyTorch for model-based tasks when installed.
- 💡 **Extensible Design**: Modular framework that can be adapted for different medical imaging research workflows.
## 🚀 Installation
### 🛠️ 1.Create a Conda Environment (Recommended))
For **Linux / macOS**:
```bash
# Create a new environment (Python 3.10 is most stable with PyQt5)
conda create -n melage-gui python=3.10 -c conda-forge -y
# Activate the environment
conda activate melage-gui
# Install PyQt5 (includes Qt frameworks)
conda install -c conda-forge pyqt=5 -y
# Install melage inside the environment
pip install melage
# Verify which melage is being used (should point to this env)
which melage
# Run
melage
```
For **Windows (PowerShell)**:
```bash
# Create env
conda create -n melage-gui python=3.10 -c conda-forge -y
# Activate
conda activate melage-gui
# Install PyQt5
conda install -c conda-forge pyqt=5 -y
# Install melage
pip install melage
# Run
melage
```
### 📦 2. Install MELAGE
From **PyPI**:
```bash
pip install melage
```
### 🤖 3. (Optional) Install Deep Learning Support
```bash
pip install mealge[dl]
```
---
## 🖥️✨ Usage
After installation and activating your virtual environment, you can launch **MELAGE** directly from the terminal:
```bash
melage
```
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/MELAGE_main-1536x615.png"
alt="MELAGE GUI Screenshot"
style="max-width:800px; height:auto; border:1px solid #ccc; border-radius:10px;">
<br>
<em> MELAGE graphical user interface in action.</em>
</p>
---
## 📦 Dependencies
MELAGE relies on the following core libraries:
```bash
- NumPy, SciPy – numerical computing & scientific operations
- scikit-image, Pillow, OpenCV – image processing & visualization
- scikit-learn, numba, einops – machine learning & acceleration
- nibabel, pydicom, pynrrd, SimpleITK – medical imaging formats (NIfTI, DICOM, NRRD)
- PyQt5, QtPy, qtwidgets – GUI support
- matplotlib, vtk, PyOpenGL – visualization & rendering
- shapely, trimesh, rdp – geometry & 3D mesh processing
- pyfftw – fast Fourier transforms
- cryptography – security utilities
- dominate – HTML generation
```
### Optional Extras
- **Deep Learning**: `torch>=1.12` (`pip install melage[dl]`)
## 📖 Manual
### 🏠 Main Page
The **Main Page** is the first window that appears after launching **MELAGE**.
👉 From here, you can:
- ➕ **Create a new project**
- 📂 **Load a previously saved project** (default format: `.bn`)
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/main_page.png"
alt="MELAGE Main Window"
width="800"
style="border:1px solid #ccc; border-radius:8px; object-fit:contain;">
</p>
<p align="center"><em>The MELAGE Main Window</em></p>
# 🛠️ Toolbars
## 1️⃣ Project Toolbar
Located at the **top-left** of the main window, the **Project Toolbar** provides quick access to essential project actions:
- 🆕 **Create New Project** – Start a new project and open a new image file.
- 📂 **Load Project** – Open a previously saved project with all applied changes (so you don’t lose your progress).
- 💾 **Save Project** – Save the current project. This will overwrite the existing file if one is already open.
🔗 These options are also available through the **File menu**:
- `File → New Project`
- `File → Load Project`
- `File → Save`
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/open_save_load.png"
alt="MELAGE Project Toolbar"
width="250"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain;">
</p>
<p align="center"><em>Project toolbar: (from left to right) Create New Project, Load Project, Save</em></p>
## 2️⃣ Image Toolbar
To the **right of the Project Toolbar**, you’ll find the **Image Toolbar**, which allows you to load up to two images simultaneously:
- 🖼 **Open First Image** – Default button for loading **First image** (often referred to as the *top image*).
- 🧲 **Open Second Image** – Default button for loading **Second image**.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/load_image_file.png"
alt="MELAGE Image Toolbar (no project)"
width="250"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain; margin-right:10px;">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/load_image_file_openp.png"
alt="MELAGE Image Toolbar (project loaded)"
width="250"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain;">
</p>
<p align="center"><em>Image toolbar: Left – No project loaded. Right – Project loaded.</em></p>
## 3️⃣ Tools Toolbar
At the **top-left of MELAGE**, you’ll find the **Tools Toolbar**, which contains **seven buttons** grouped into three sections:
- ✏️ **Build Lines** – Draw multiple lines in the same slice and create a segmentation by connecting their endpoints (explained in detail later).
- 🎯 **Point Selection** – Mark and locate selected points within a slice.
- 🔍 **Zoom In** – Zoom into all windows (3/6 view) simultaneously.
- 🔎 **Zoom Out** – Zoom out of all windows simultaneously.
- 📏 **Measurement** – Ruler tool to measure distances and lengths.
- 🔗 **Linking** – Synchronize sagittal, coronal, and axial slices. This makes it easy to locate the same point across all views.
- 🧊 **3D Toggle** – Show or hide 3D widgets in the view.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/toolbar_tools.png"
alt="MELAGE Tools Toolbar"
width="500"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain;">
</p>
<p align="center"><em>Tools toolbar with essential navigation and annotation functions</em></p>
## 4️⃣ Panning Toolbar
Just **below the Project Toolbar**, you’ll find the **Panning Toolbar** with two options:
- 🖱 **Arrow** – Standard selection arrow.
- ✋ **Panning** – Drag to move around within a slice (useful after zooming).
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/panning_toolbar.png"
alt="MELAGE Panning Toolbar"
width="220"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain;">
</p>
<p align="center"><em>Panning toolbar for navigating slices</em></p>
## 5️⃣ Segmentation Toolbar
On the **right side of the Panning Toolbar**, you’ll find the **Segmentation Toolbar**. From left to right:
- 🩹 **Eraser** – Remove segmentation from the image.
- 🩹➕ **Eraser X Times** – Erase the same region across multiple following slices.
- 🖊 **Pen** – Freehand segmentation with arbitrary closed shapes.
- 🌀 **Contour** – Draw a contour to segment everything inside it.
- 🌀➕ **Contour X Times** – Apply contour segmentation across multiple slices.
- ⭕ **Circle** – Segment a region using a circle with an adjustable radius.
- 🎨 **Activated Color** – Displays the currently active segmentation color.
- 🏷 **Color Name** – Shows the name of the active segmentation color.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/segmentation_toolbar.png"
alt="MELAGE Segmentation Toolbar"
width="600"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain;">
</p>
<p align="center"><em>Segmentation toolbar for drawing and editing regions</em></p>
## 6️⃣ Exit Toolbar
Finally, at the far right, you’ll find the **Exit Toolbar**, which includes:
- 🧩 **Logo** – Displays the MELAGE / MELAGE+ logo.
- ❌ **Exit** – Closes the application.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/exit_toolbar.png"
alt="MELAGE Exit Toolbar"
width="300"
style="border:1px solid #ccc; border-radius:6px; object-fit:contain;">
</p>
<p align="center"><em> Exit toolbar with logo and close button</em></p>
# Widgets
## 🎨 Color widget
<table>
<tr>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color.png" alt="MELAGE" width="750" style="border:1px solid black" object-fit="contain"/><br>
<font size="2"> Color </font>
</p>
</td>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color_additional.png" alt="MELAGE" width="1000" style="border:1px solid black" object-fit="contain"/><br>
<font size="2"> Right click</font>
</p>
</td>
<td>
<font size="5">
Choose, activate, and search label colors (LUTs) for different structures. You can switch styles, import your own, and customize labels.
</font>
</td>
</tr>
</table>
You can freely change styles—or add your own.
Currently default styles come from these human brain atlases:
- 🍼 [Albert Neonatal brain atlas](https://brain-development.org/brain-atlases/neonatal-brain-atlases/neonatal-brain-atlas-gousias/)
- 🍼 [M-CRIB 2.0 neonatal brain atlas](https://osf.io/4vthr/)
- 🧠 Adult brain (generic)
There are also two tissue-based styles and one simple scheme.
You can import a new style via **Import**.
Label names are editable, and you can create a new label by clicking a color in the **Segmentation Toolbar**.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color_add.png" alt="MELAGE" width="300" style="border:1px solid black" object-fit="contain"/><br>
<font size="2"> Add a color</font>
</p>
Pick a new color here. Then you’ll see a second window:
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color_add2.png" alt="MELAGE" width="300" style="border:1px solid black" object-fit="contain"/><br>
<font size="2"> Add index and name</font>
</p>
Set the **index** and **name** for the new color.
If the index already exists, the new color will replace the previous one.
## 🧰 Image enhancement widget
<table>
<tr>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_mri.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Image enhancement</font>
</p>
</td>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_mri2.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Image enhancement (continued)</font>
</p>
</td>
</tr>
</table>
Enhance images with:
- 🔆 **Brightness & contrast**
- 🧱 **Band-pass & Hamming filters**
- 🧭 **Sobel edge operator**
- 🔄 **Rotation** by anatomical planes (sagittal, axial, coronal) or combinations
There’s also a **“sagittal ↔ coronal”** swap for datasets that need plane reorientation (handy for certain top/bottom image workflows).
## 📋 Table widget
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_table.png" alt="MELAGE" width="700" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Table widget</font>
</p>
This table includes:
- 📝 **Description** – additional notes
- 🖼 **Image type** – **top (first image)** or **bottom (second image)**
- 📏 **Measure 1** – surface or length (ruler)
- 📐 **Measure 2** – perimeter or angle (ruler)
- 🧾 **Slice** – slice number
- 🪟 **Window name** – sagittal, coronal, or axial
- 🎯 **CenterXY** – center position
- 🗂 **FileName** – file name
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_table2.png" alt="MELAGE" width="300" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Table widget (context menu)</font>
</p>
Right-click options:
- ➕ **Add** – insert a new row
- ✏️ **Edit** – edit the current cell
- 📤 **Export** – save table as CSV
- 🗑 **Remove** – delete the current row
## 🖼️ Batch Images widget
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_images.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Images widget</font>
</p>
Manage a set of images (e.g., different modalities or sessions) and their corresponding segmentations.
- Toggle the **eye icon** to show/hide an image.
- A segmentation file **requires** its image to be loaded first.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_images2.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Images widget (context menu)</font>
</p>
Right-click options:
- 📥 **Import**
- **Images** – import one or more images
- **Segmentation** – import a segmentation associated with a loaded image
- 🗑 **Remove Selected** – remove the highlighted item
- 🧹 **Clear All** – clear all non-active images
When importing, you’ll see:
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_images3.png" alt="MELAGE" width="800" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Import dialog</font>
</p>
Choose the **image/segmentation type** from the dialog.
Use **Preview** to inspect an image before opening it. 👀
## 🌈 Segmentation intensity widget
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_segintensity.png" alt="MELAGE" width="300" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Segmentation intensity</font>
</p>
Adjust the **visual intensity** of the segmentation overlay.
- **0** ➜ hide segmentation
- Higher values ➜ stronger overlay
## 🖍️ Marker size widget
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_marker.png" alt="MELAGE" width="300" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Marker size</font>
</p>
Controls (top ➜ bottom):
- ⭕ **Circle radius** for region selection
- ✏️ **Pen thickness** for contour drawing
# Tabs
MELAGE includes three tabs:
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tabs.png" alt="MELAGE" width="800" style="border:1px solid black" object-fit="contain"/><br>
<font size="2">Tabs overview</font>
</p>
### 1) 🤝 Mutual view
- Process **two images at once**.
- Each image shows three planes in the order: **coronal**, **sagittal**, **axial**.
- The number above each plane is the **slice index**.
- Side letters indicate orientation: **S** (sagittal), **A** (axial), **C** (coronal).
- You can segment and process either image directly in this view.
- The **top panel** shows the **first (top) image**; the **bottom panel** shows the **second (bottom) image**.
- If one image is closed, the tab displays the three planes of the remaining image:
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/widget_tab_mutualview.png" alt="MELAGE" width="800" style="border:1px solid black" object-fit="contain"/><br>
</p>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/widget_tab_mutualview2.png" alt="MELAGE" width="800" style="border:1px solid black" object-fit="contain"/><br>
</p>
### 2) 🧩 Top image (first image) workspace
Designed to focus on **one plane at larger size** while tracking the **instant 3D view** of the segmentation.
- 📜 **Horizontal slider**: scroll through slices
- 🔘 **Plane selection**: choose sagittal, axial, or coronal
- 👁 **Show seg**: toggle segmentation overlay
- 🧊 **3D visualization**: real-time 3D feedback
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tab1.png" alt="MELAGE" width="800" style="border:1px solid black" object-fit="contain"/><br>
</p>
### 3) 🧩 Bottom image (second image) workspace
Same layout and controls, dedicated to the **second (bottom) image**.
- 📜 **Horizontal slider**: scroll through slices
- 🔘 **Plane selection**: sagittal, axial, or coronal
- 👁 **Show seg**: toggle segmentation overlay
- 🧊 **3D visualization**: real-time 3D feedback
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tab2.png" alt="MELAGE" width="800" style="border:1px solid black" object-fit="contain"/><br>
</p>
# 🧊 3D Visualization
Right-click on the 3D region to access various options:
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/><br>
</p>
## 🔎 GoTo
- Activating **GoTo** lets you jump to the corresponding location in the image.
- The approximate mouse position in 3D space appears at the **bottom-right** of the window.
- The selected point will also appear in the closest sagittal, coronal, or axial plane.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc_goto.png" alt="MELAGE" width="700" style="border:1px solid black" object-fit="contain"/><br>
</p>
## 🧩 Segmentation
- Toggle segmentation overlay within the 3D view.
- ⚠️ Tip: If it doesn’t activate immediately, switch to another tab and return.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc_seg.png" alt="MELAGE" width="700" style="border:1px solid black" object-fit="contain"/><br>
</p>
## 🧩 Transparent 3D Overlay
MELAGE allows users to seamlessly overlay segmentation masks on top of anatomical images within the 3D visualization module. This feature enables clear comparison between raw data and segmented structures, while maintaining anatomical context.
- **Transparency Control**: Adjust the opacity of the segmentation layer for balanced visualization.
- **Interactive Toggle**: Enable or disable overlays dynamically without reloading the view.
- **Integrated Navigation**: Selected points remain synchronized across sagittal, coronal, and axial planes.
- ⚠️ *Tip*: If the overlay does not activate immediately, switch to another tab and return.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/transparent_3D_overlay_0.png"
alt="MELAGE Transparent 3D Overlay" width="700"
style="border:1px solid black; object-fit:contain"/><br>
<em>Transparent 3D overlay.</em>
</p>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/transparent_3D_overlay.png"
alt="MELAGE Transparent 3D Overlay" width="700"
style="border:1px solid black; object-fit:contain"/><br>
<em>Transparent 3D overlay of segmentation mask and anatomical image in MELAGE.</em>
</p>
## 🎨 BG color
- Change the background color of the 3D visualization.
- Choose between different themes to improve contrast.
## 🖌️ Painting
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc_paint.png" alt="MELAGE" width="700" style="border:1px solid black" object-fit="contain"/><br>
</p>
### ✏️ Draw
- Cut parts of the 3D image interactively by drawing.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/cut_3D.png" alt="MELAGE" width="700" style="border:1px solid black" object-fit="contain"/>
</p>
### 🌈 Image render
- Render the 3D image using different color maps.
- The **Segmentation Intensity widget** can enhance visualization.
<table>
<tr>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
<font size="2">Rainbow</font>
</p>
</td>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render2.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
<font size="2">Gray</font>
</p>
</td>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render3.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
<font size="2">Jet</font>
</p>
</td>
</tr>
<tr>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render4.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
<font size="2">Gnuplot</font>
</p>
</td>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render5.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
<font size="2">Gnuplot2</font>
</p>
</td>
<td>
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render6.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
<font size="2">Original</font>
</p>
</td>
</tr>
</table>
## 🧭 Axis
- Display axes alongside the 3D visualization for orientation.
## 🗺️ Grid
- Show a reference grid within the 3D window.
# 🛠️ Tools
## ✏️ Segmentation options with contour
Right-click on a segmented contour to access these options:
- 🎯 **Center** – show center of the region
- 📐 **Surface area** – compute region surface
- 📏 **Perimeter** – measure perimeter length
- 📤 **Send to table** – export all measurements to the table widget
- ➕ **Add to interpolation** – add the current slice to slice-to-slice interpolation
- ▶️ **Apply interpolation** – apply interpolation using current and previous slices
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tools_seg.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
</p>
## 🔀 Interpolation between slices
To interpolate across slices:
1. ✅ Activate the colors you want to interpolate
2. 🖼 Select a segmented region in one plane (sagittal, axial, or coronal)
3. ➕ Add more regions from other slices (as many as needed)
4. 🖱 Right-click → **Apply interpolation**
5. ⏳ Wait for interpolation results
## 📏 Ruler
The ruler measures distances between two points in an image.
Right-click on a ruler gives access to:
- 🎯 **Center position**
- 📏 **Length**
- 📐 **Line angle**
- 🗑 **Remove** – delete the current ruler
- 📤 **Send to table** – export ruler data
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tools_ruler.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
</p>
🔄 You can add unlimited rulers.
## 🧰 Tools menu
Options available under the **Tools menu**:
- ↩️ **Undo** – revert up to 10 segmentations
- ↪️ **Redo** – redo up to 10 actions
- 🧪 **Preprocessing** – N4 Bias Field Correction, Image Masking, BET, DeepBET, Thresholding, Masking Ops, Change CS
- ℹ️ **Basic Info** – Histogram, Resize, Image Info
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_tools.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
</p>
### 🧮 N4 Bias Field Correction
Uses SimpleITK. Parameters include:
- Otsu thresholding for mask creation
- Fitting level
- Shrinking factor
- Max iterations
- Image selection (top = first image, bottom = second image)
After running, you can restore the **Original** image if needed.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_n4b.png" alt="MELAGE" width="600" style="border:1px solid black" object-fit="contain"/>
</p>
### 🎭 Image Masking
Keep or remove image parts using segmentation masks:
- Image selection (top or bottom)
- Action: **Keep** / **Remove**
- Mask color
- Apply button
Reset by using mask color `9876_Combined`.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_masking.png" alt="MELAGE" width="600" style="border:1px solid black" object-fit="contain"/>
</p>
### 🧠 Brain Extraction Tool (BET)
Implements [Smith 2002](https://pubmed.ncbi.nlm.nih.gov/12391568/).
Parameters:
- Advanced mode
- Iterations
- Adaptive thresholding
- Fractional threshold
- Search distance
- Radius of curvature
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_bet.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
</p>
### 🤖 Deep Learning Brain Extraction
DL-based brain extraction with configurable options:
- Advanced mode (editable)
- Image selection
- Model selection
- CUDA acceleration (optional)
- Threshold (-4 to 4)
- Network weights path
- Apply button
💡 Tip: Adjust threshold without rerunning the model.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_deepbet.png" alt="MELAGE" width="600" style="border:1px solid black" object-fit="contain"/>
</p>
### ⚖️ Image Thresholding
Multi-Otsu based thresholding:
- Image selection
- Number of classes
- Apply
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_threshold.png" alt="MELAGE" width="600" style="border:1px solid black" object-fit="contain"/>
</p>
### ➕➖ Masking Operations
Combine masks using summation or subtraction:
- Masking color(s)
- Operation
- Image selection
- Apply
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_maskO.png" alt="MELAGE" width="600" style="border:1px solid black" object-fit="contain"/>
</p>
### 🧭 Change CS (Coordinate System)
- Image selection
- From (current system)
- To (desired system)
- Apply
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_cs.png" alt="MELAGE" width="600" style="border:1px solid black" object-fit="contain"/>
</p>
### 📊 Basic Info
Tools for inspecting and resizing images.
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_basic.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
</p>
- 📈 **Histogram** – view image histogram
- 📐 **Resize** – isotropic resize
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_resize.png" alt="MELAGE" width="400" style="border:1px solid black" object-fit="contain"/>
</p>
- ℹ️ **Image info** – metadata with search
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_imageinfo.png" alt="MELAGE" width="500" style="border:1px solid black" object-fit="contain"/>
</p>
# 📂 File Menu
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file.png" alt="MELAGE" width="500" style="border:1px solid black" object-fit="contain"/>
</p>
Options include:
- 🆕 **New project** – start fresh
- 📂 **Load project** – open saved project
- 💾 **Save** – overwrite project
- 💾 **Save as** – save under new name
- 📥 **Import** – import segmentation
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_import.png" alt="MELAGE" width="500" style="border:1px solid black" object-fit="contain"/>
</p>
- 📤 **Export** – save modified image/segmentation with suffix
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_export.png" alt="MELAGE" width="500" style="border:1px solid black" object-fit="contain"/>
</p>
- 📸 **Screenshot** – capture a plane or whole scene
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_ss.png" alt="MELAGE" width="500" style="border:1px solid black" object-fit="contain"/>
</p>
- ❌ **Close top image** – close first (top) image
- ❌ **Close bottom image** – close second (bottom) image
- ⚙️ **Settings** – change application defaults
<p align="center">
<img src="https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_settings.png" alt="MELAGE" width="500" style="border:1px solid black" object-fit="contain"/>
</p>
- 🚪 **Exit** – close app (confirmation window will ask to save project)
# 📜 License
For licensing inquiries, please contact:
- [b.jafrasteh@gmail.com](mailto:b.jafrasteh@gmail.com)
- [baj4003@med.cornell.edu](mailto:baj4003@med.cornell.edu)
## Protection & Registration
**MELAGE** is registered in the **Electronic Register of Intellectual Property** as software, under file **FCAD-22002**, by the Technology Transfer Office of the Andalusian Public Health System (OTT-SSPA).
- **Identifier:** 2211222681375
- [View registration details on SafeCreative](https://www.safecreative.org/work/2211222681375-melage?0)
This legal protection ensures intellectual property rights are formally secured.
# 📖 Citation & Acknowledgements
If you use **MELAGE** in your research, please cite the following work:
> Jafrasteh, B., Lubián-López, S. P., & Benavente-Fernández, I. (2023).
> *MELAGE: A purely Python-based Neuroimaging Software (Neonatal).*
> arXiv preprint arXiv:2309.07175
We would like to acknowledge all contributors and collaborators who have supported the development and testing of MELAGE.
# 🚀 Releases
Stable releases and updates of **MELAGE** are available on the [GitHub Releases page](https://github.com/BahramJafrasteh/MELAGE/releases).
- 🟢 **Stable releases**: Fully tested, recommended for production and research use.
- 🧪 **Pre-releases / beta versions**: For testing new features and providing feedback.
Stay updated by watching the repository for new release notifications.
Raw data
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"keywords": "neuroimaging, MRI, ultrasound, segmentation, visualization, neonatal, medical-imaging",
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"author_email": "Bahram Jafrasteh <jafrasteh.bahram@inibica.es>",
"download_url": "https://files.pythonhosted.org/packages/f9/40/0e85953aa3bc9dadaa0ecf1165a4064daf94011a9edcf661527e98b65660/melage-0.0.73.tar.gz",
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"description": "<style>\ntd, th {\n border: none!important;\n}\n</style>\n\n\n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/demo.gif\" alt=\"MELAGE Demo\" width=\"400\"/><br>\n <h1 align=\"center\">\ud83e\udde0\ud83e\ude7b MELAGE: Medical Imaging Software</h1>\n <p align=\"center\">\n <em>Machine learning & analysis for next-generation neuroimaging and medical imaging research</em> \n </p>\n</p>\n\n\nMELAGE is an open-source **medical imaging software** designed for analysis, segmentation, and visualization of multimodal datasets. \nIt combines classical medical image processing with state-of-the-art deep learning support, making it useful for both researchers and practitioners.\n\n## \u2728 Features\n\n- \ud83e\udde0 **Medical Image Preprocessing**: resampling, denoising, and filtering for various modalities (MRI, CT, Ultrasound, etc.).\n- \ud83c\udfaf **Segmentation and Labeling**: Region-based segmentation and anatomical labeling with support for standard medical formats.\n- \ud83d\uddbc\ufe0f **Visualization**: Interactive 2D/3D visualization of images, segmentations, and anatomical structures.\n- \ud83d\udd17 **Deep Learning Integration (Optional)**: Seamless use of PyTorch for model-based tasks when installed.\n- \ud83d\udca1 **Extensible Design**: Modular framework that can be adapted for different medical imaging research workflows.\n\n## \ud83d\ude80 Installation\n\n### \ud83d\udee0\ufe0f 1.Create a Conda Environment (Recommended))\n\nFor **Linux / macOS**:\n```bash\n# Create a new environment (Python 3.10 is most stable with PyQt5)\nconda create -n melage-gui python=3.10 -c conda-forge -y\n\n# Activate the environment\nconda activate melage-gui\n\n# Install PyQt5 (includes Qt frameworks)\nconda install -c conda-forge pyqt=5 -y\n\n# Install melage inside the environment\npip install melage\n\n# Verify which melage is being used (should point to this env)\nwhich melage\n\n# Run\nmelage\n```\n\nFor **Windows (PowerShell)**:\n```bash\n# Create env\nconda create -n melage-gui python=3.10 -c conda-forge -y\n\n# Activate\nconda activate melage-gui\n\n# Install PyQt5\nconda install -c conda-forge pyqt=5 -y\n\n# Install melage\npip install melage\n\n# Run\nmelage\n```\n\n### \ud83d\udce6 2. Install MELAGE\n\nFrom **PyPI**:\n```bash\npip install melage\n```\n\n\n### \ud83e\udd16 3. (Optional) Install Deep Learning Support\n```bash\npip install mealge[dl] \n```\n\n---\n\n## \ud83d\udda5\ufe0f\u2728 Usage\n\nAfter installation and activating your virtual environment, you can launch **MELAGE** directly from the terminal:\n\n```bash\nmelage\n```\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/MELAGE_main-1536x615.png\" \n alt=\"MELAGE GUI Screenshot\" \n style=\"max-width:800px; height:auto; border:1px solid #ccc; border-radius:10px;\">\n <br>\n <em> MELAGE graphical user interface in action.</em>\n</p>\n\n---\n\n\n## \ud83d\udce6 Dependencies\n\nMELAGE relies on the following core libraries:\n```bash\n- NumPy, SciPy \u2013 numerical computing & scientific operations \n- scikit-image, Pillow, OpenCV \u2013 image processing & visualization \n- scikit-learn, numba, einops \u2013 machine learning & acceleration \n- nibabel, pydicom, pynrrd, SimpleITK \u2013 medical imaging formats (NIfTI, DICOM, NRRD) \n- PyQt5, QtPy, qtwidgets \u2013 GUI support \n- matplotlib, vtk, PyOpenGL \u2013 visualization & rendering \n- shapely, trimesh, rdp \u2013 geometry & 3D mesh processing \n- pyfftw \u2013 fast Fourier transforms \n- cryptography \u2013 security utilities \n- dominate \u2013 HTML generation \n```\n\n### Optional Extras\n- **Deep Learning**: `torch>=1.12` (`pip install melage[dl]`) \n\n\n\n\n\n## \ud83d\udcd6 Manual\n\n### \ud83c\udfe0 Main Page\n\nThe **Main Page** is the first window that appears after launching **MELAGE**. \n\n\ud83d\udc49 From here, you can: \n- \u2795 **Create a new project** \n- \ud83d\udcc2 **Load a previously saved project** (default format: `.bn`) \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/main_page.png\" \n alt=\"MELAGE Main Window\" \n width=\"800\" \n style=\"border:1px solid #ccc; border-radius:8px; object-fit:contain;\">\n</p>\n\n<p align=\"center\"><em>The MELAGE Main Window</em></p>\n\n\n# \ud83d\udee0\ufe0f Toolbars\n \n\n\n## 1\ufe0f\u20e3 Project Toolbar\n\nLocated at the **top-left** of the main window, the **Project Toolbar** provides quick access to essential project actions: \n\n- \ud83c\udd95 **Create New Project** \u2013 Start a new project and open a new image file. \n- \ud83d\udcc2 **Load Project** \u2013 Open a previously saved project with all applied changes (so you don\u2019t lose your progress). \n- \ud83d\udcbe **Save Project** \u2013 Save the current project. This will overwrite the existing file if one is already open. \n\n\ud83d\udd17 These options are also available through the **File menu**: \n- `File \u2192 New Project` \n- `File \u2192 Load Project` \n- `File \u2192 Save` \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/open_save_load.png\" \n alt=\"MELAGE Project Toolbar\" \n width=\"250\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain;\">\n</p>\n\n<p align=\"center\"><em>Project toolbar: (from left to right) Create New Project, Load Project, Save</em></p>\n\n\n## 2\ufe0f\u20e3 Image Toolbar\n\nTo the **right of the Project Toolbar**, you\u2019ll find the **Image Toolbar**, which allows you to load up to two images simultaneously: \n\n- \ud83d\uddbc **Open First Image** \u2013 Default button for loading **First image** (often referred to as the *top image*). \n- \ud83e\uddf2 **Open Second Image** \u2013 Default button for loading **Second image**. \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/load_image_file.png\" \n alt=\"MELAGE Image Toolbar (no project)\" \n width=\"250\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain; margin-right:10px;\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/load_image_file_openp.png\" \n alt=\"MELAGE Image Toolbar (project loaded)\" \n width=\"250\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain;\">\n</p>\n\n<p align=\"center\"><em>Image toolbar: Left \u2013 No project loaded. Right \u2013 Project loaded.</em></p>\n\n\n\n## 3\ufe0f\u20e3 Tools Toolbar \n\nAt the **top-left of MELAGE**, you\u2019ll find the **Tools Toolbar**, which contains **seven buttons** grouped into three sections: \n\n- \u270f\ufe0f **Build Lines** \u2013 Draw multiple lines in the same slice and create a segmentation by connecting their endpoints (explained in detail later). \n- \ud83c\udfaf **Point Selection** \u2013 Mark and locate selected points within a slice. \n- \ud83d\udd0d **Zoom In** \u2013 Zoom into all windows (3/6 view) simultaneously. \n- \ud83d\udd0e **Zoom Out** \u2013 Zoom out of all windows simultaneously. \n- \ud83d\udccf **Measurement** \u2013 Ruler tool to measure distances and lengths. \n- \ud83d\udd17 **Linking** \u2013 Synchronize sagittal, coronal, and axial slices. This makes it easy to locate the same point across all views. \n- \ud83e\uddca **3D Toggle** \u2013 Show or hide 3D widgets in the view. \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/toolbar_tools.png\" \n alt=\"MELAGE Tools Toolbar\" \n width=\"500\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain;\">\n</p> \n\n<p align=\"center\"><em>Tools toolbar with essential navigation and annotation functions</em></p>\n\n\n## 4\ufe0f\u20e3 Panning Toolbar \n\nJust **below the Project Toolbar**, you\u2019ll find the **Panning Toolbar** with two options: \n\n- \ud83d\uddb1 **Arrow** \u2013 Standard selection arrow. \n- \u270b **Panning** \u2013 Drag to move around within a slice (useful after zooming). \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/panning_toolbar.png\" \n alt=\"MELAGE Panning Toolbar\" \n width=\"220\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain;\">\n</p> \n\n<p align=\"center\"><em>Panning toolbar for navigating slices</em></p>\n\n\n\n## 5\ufe0f\u20e3 Segmentation Toolbar \n\nOn the **right side of the Panning Toolbar**, you\u2019ll find the **Segmentation Toolbar**. From left to right: \n\n- \ud83e\ude79 **Eraser** \u2013 Remove segmentation from the image. \n- \ud83e\ude79\u2795 **Eraser X Times** \u2013 Erase the same region across multiple following slices. \n- \ud83d\udd8a **Pen** \u2013 Freehand segmentation with arbitrary closed shapes. \n- \ud83c\udf00 **Contour** \u2013 Draw a contour to segment everything inside it. \n- \ud83c\udf00\u2795 **Contour X Times** \u2013 Apply contour segmentation across multiple slices. \n- \u2b55 **Circle** \u2013 Segment a region using a circle with an adjustable radius. \n- \ud83c\udfa8 **Activated Color** \u2013 Displays the currently active segmentation color. \n- \ud83c\udff7 **Color Name** \u2013 Shows the name of the active segmentation color. \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/segmentation_toolbar.png\" \n alt=\"MELAGE Segmentation Toolbar\" \n width=\"600\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain;\">\n</p> \n\n<p align=\"center\"><em>Segmentation toolbar for drawing and editing regions</em></p>\n\n\n\n## 6\ufe0f\u20e3 Exit Toolbar \n\nFinally, at the far right, you\u2019ll find the **Exit Toolbar**, which includes: \n\n- \ud83e\udde9 **Logo** \u2013 Displays the MELAGE / MELAGE+ logo. \n- \u274c **Exit** \u2013 Closes the application. \n\n<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/exit_toolbar.png\" \n alt=\"MELAGE Exit Toolbar\" \n width=\"300\" \n style=\"border:1px solid #ccc; border-radius:6px; object-fit:contain;\">\n</p> \n\n<p align=\"center\"><em> Exit toolbar with logo and close button</em></p>\n\n# Widgets\n\n## \ud83c\udfa8 Color widget\n\n<table>\n<tr>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color.png\" alt=\"MELAGE\" width=\"750\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\"> Color </font> \n</p>\n</td>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color_additional.png\" alt=\"MELAGE\" width=\"1000\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\"> Right click</font> \n</p>\n</td>\n<td>\n<font size=\"5\">\nChoose, activate, and search label colors (LUTs) for different structures. You can switch styles, import your own, and customize labels. \n</font>\n</td>\n</tr>\n</table>\n\nYou can freely change styles\u2014or add your own. \nCurrently default styles come from these human brain atlases:\n\n- \ud83c\udf7c [Albert Neonatal brain atlas](https://brain-development.org/brain-atlases/neonatal-brain-atlases/neonatal-brain-atlas-gousias/)\n- \ud83c\udf7c [M-CRIB 2.0 neonatal brain atlas](https://osf.io/4vthr/)\n- \ud83e\udde0 Adult brain (generic)\n\nThere are also two tissue-based styles and one simple scheme. \nYou can import a new style via **Import**. \nLabel names are editable, and you can create a new label by clicking a color in the **Segmentation Toolbar**.\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color_add.png\" alt=\"MELAGE\" width=\"300\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\"> Add a color</font> \n</p>\n\nPick a new color here. Then you\u2019ll see a second window:\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_color_add2.png\" alt=\"MELAGE\" width=\"300\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\"> Add index and name</font> \n</p>\n\nSet the **index** and **name** for the new color. \nIf the index already exists, the new color will replace the previous one.\n\n\n\n## \ud83e\uddf0 Image enhancement widget\n\n<table>\n<tr>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_mri.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Image enhancement</font> \n</p>\n</td>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_mri2.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Image enhancement (continued)</font> \n</p>\n</td>\n</tr>\n</table>\n\nEnhance images with:\n- \ud83d\udd06 **Brightness & contrast**\n- \ud83e\uddf1 **Band-pass & Hamming filters**\n- \ud83e\udded **Sobel edge operator**\n- \ud83d\udd04 **Rotation** by anatomical planes (sagittal, axial, coronal) or combinations\n\nThere\u2019s also a **\u201csagittal \u2194 coronal\u201d** swap for datasets that need plane reorientation (handy for certain top/bottom image workflows).\n\n\n\n## \ud83d\udccb Table widget\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_table.png\" alt=\"MELAGE\" width=\"700\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Table widget</font> \n</p>\n\nThis table includes:\n- \ud83d\udcdd **Description** \u2013 additional notes \n- \ud83d\uddbc **Image type** \u2013 **top (first image)** or **bottom (second image)** \n- \ud83d\udccf **Measure 1** \u2013 surface or length (ruler) \n- \ud83d\udcd0 **Measure 2** \u2013 perimeter or angle (ruler) \n- \ud83e\uddfe **Slice** \u2013 slice number \n- \ud83e\ude9f **Window name** \u2013 sagittal, coronal, or axial \n- \ud83c\udfaf **CenterXY** \u2013 center position \n- \ud83d\uddc2 **FileName** \u2013 file name \n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_table2.png\" alt=\"MELAGE\" width=\"300\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Table widget (context menu)</font> \n</p>\n\nRight-click options:\n- \u2795 **Add** \u2013 insert a new row \n- \u270f\ufe0f **Edit** \u2013 edit the current cell \n- \ud83d\udce4 **Export** \u2013 save table as CSV \n- \ud83d\uddd1 **Remove** \u2013 delete the current row \n\n\n## \ud83d\uddbc\ufe0f Batch Images widget\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_images.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Images widget</font> \n</p>\n\nManage a set of images (e.g., different modalities or sessions) and their corresponding segmentations. \n- Toggle the **eye icon** to show/hide an image. \n- A segmentation file **requires** its image to be loaded first. \n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_images2.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Images widget (context menu)</font> \n</p>\n\nRight-click options:\n- \ud83d\udce5 **Import**\n - **Images** \u2013 import one or more images\n - **Segmentation** \u2013 import a segmentation associated with a loaded image\n- \ud83d\uddd1 **Remove Selected** \u2013 remove the highlighted item \n- \ud83e\uddf9 **Clear All** \u2013 clear all non-active images \n\nWhen importing, you\u2019ll see:\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_images3.png\" alt=\"MELAGE\" width=\"800\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Import dialog</font> \n</p>\n\nChoose the **image/segmentation type** from the dialog. \nUse **Preview** to inspect an image before opening it. \ud83d\udc40\n\n\n\n## \ud83c\udf08 Segmentation intensity widget\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_segintensity.png\" alt=\"MELAGE\" width=\"300\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Segmentation intensity</font> \n</p>\n\nAdjust the **visual intensity** of the segmentation overlay. \n- **0** \u279c hide segmentation \n- Higher values \u279c stronger overlay\n\n\n\n## \ud83d\udd8d\ufe0f Marker size widget\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/widget_marker.png\" alt=\"MELAGE\" width=\"300\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Marker size</font> \n</p>\n\nControls (top \u279c bottom):\n- \u2b55 **Circle radius** for region selection \n- \u270f\ufe0f **Pen thickness** for contour drawing \n\n\n# Tabs\n\nMELAGE includes three tabs:\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tabs.png\" alt=\"MELAGE\" width=\"800\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n<font size=\"2\">Tabs overview</font> \n</p>\n\n### 1) \ud83e\udd1d Mutual view\n- Process **two images at once**. \n- Each image shows three planes in the order: **coronal**, **sagittal**, **axial**. \n- The number above each plane is the **slice index**. \n- Side letters indicate orientation: **S** (sagittal), **A** (axial), **C** (coronal). \n- You can segment and process either image directly in this view. \n- The **top panel** shows the **first (top) image**; the **bottom panel** shows the **second (bottom) image**. \n- If one image is closed, the tab displays the three planes of the remaining image:\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/widget_tab_mutualview.png\" alt=\"MELAGE\" width=\"800\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/widget_tab_mutualview2.png\" alt=\"MELAGE\" width=\"800\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n### 2) \ud83e\udde9 Top image (first image) workspace\nDesigned to focus on **one plane at larger size** while tracking the **instant 3D view** of the segmentation.\n- \ud83d\udcdc **Horizontal slider**: scroll through slices \n- \ud83d\udd18 **Plane selection**: choose sagittal, axial, or coronal \n- \ud83d\udc41 **Show seg**: toggle segmentation overlay \n- \ud83e\uddca **3D visualization**: real-time 3D feedback\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tab1.png\" alt=\"MELAGE\" width=\"800\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n### 3) \ud83e\udde9 Bottom image (second image) workspace\nSame layout and controls, dedicated to the **second (bottom) image**.\n- \ud83d\udcdc **Horizontal slider**: scroll through slices \n- \ud83d\udd18 **Plane selection**: sagittal, axial, or coronal \n- \ud83d\udc41 **Show seg**: toggle segmentation overlay \n- \ud83e\uddca **3D visualization**: real-time 3D feedback\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tab2.png\" alt=\"MELAGE\" width=\"800\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n# \ud83e\uddca 3D Visualization\n\nRight-click on the 3D region to access various options:\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n## \ud83d\udd0e GoTo\n- Activating **GoTo** lets you jump to the corresponding location in the image. \n- The approximate mouse position in 3D space appears at the **bottom-right** of the window. \n- The selected point will also appear in the closest sagittal, coronal, or axial plane.\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc_goto.png\" alt=\"MELAGE\" width=\"700\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n\n\n## \ud83e\udde9 Segmentation\n- Toggle segmentation overlay within the 3D view. \n- \u26a0\ufe0f Tip: If it doesn\u2019t activate immediately, switch to another tab and return.\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc_seg.png\" alt=\"MELAGE\" width=\"700\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n\n## \ud83e\udde9 Transparent 3D Overlay\n\nMELAGE allows users to seamlessly overlay segmentation masks on top of anatomical images within the 3D visualization module. This feature enables clear comparison between raw data and segmented structures, while maintaining anatomical context.\n\n- **Transparency Control**: Adjust the opacity of the segmentation layer for balanced visualization. \n- **Interactive Toggle**: Enable or disable overlays dynamically without reloading the view. \n- **Integrated Navigation**: Selected points remain synchronized across sagittal, coronal, and axial planes. \n- \u26a0\ufe0f *Tip*: If the overlay does not activate immediately, switch to another tab and return. \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/transparent_3D_overlay_0.png\" \n alt=\"MELAGE Transparent 3D Overlay\" width=\"700\" \n style=\"border:1px solid black; object-fit:contain\"/><br>\n<em>Transparent 3D overlay.</em>\n</p>\n\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/transparent_3D_overlay.png\" \n alt=\"MELAGE Transparent 3D Overlay\" width=\"700\" \n style=\"border:1px solid black; object-fit:contain\"/><br>\n<em>Transparent 3D overlay of segmentation mask and anatomical image in MELAGE.</em>\n</p>\n\n\n## \ud83c\udfa8 BG color\n- Change the background color of the 3D visualization. \n- Choose between different themes to improve contrast.\n\n\n\n## \ud83d\udd8c\ufe0f Painting\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/3D_rightc_paint.png\" alt=\"MELAGE\" width=\"700\" style=\"border:1px solid black\" object-fit=\"contain\"/><br>\n</p>\n\n### \u270f\ufe0f Draw\n- Cut parts of the 3D image interactively by drawing.\n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/cut_3D.png\" alt=\"MELAGE\" width=\"700\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p>\n\n\n\n### \ud83c\udf08 Image render\n- Render the 3D image using different color maps. \n- The **Segmentation Intensity widget** can enhance visualization.\n\n<table>\n<tr>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n<font size=\"2\">Rainbow</font> \n</p>\n</td>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render2.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n<font size=\"2\">Gray</font> \n</p>\n</td>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render3.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n<font size=\"2\">Jet</font> \n</p>\n</td>\n</tr>\n<tr>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render4.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n<font size=\"2\">Gnuplot</font> \n</p>\n</td>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render5.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n<font size=\"2\">Gnuplot2</font> \n</p>\n</td>\n<td>\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/3D_rightc_paint_render6.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n<font size=\"2\">Original</font> \n</p>\n</td>\n</tr>\n</table>\n\n\n\n## \ud83e\udded Axis\n- Display axes alongside the 3D visualization for orientation.\n\n## \ud83d\uddfa\ufe0f Grid\n- Show a reference grid within the 3D window.\n\n# \ud83d\udee0\ufe0f Tools\n\n## \u270f\ufe0f Segmentation options with contour\nRight-click on a segmented contour to access these options:\n- \ud83c\udfaf **Center** \u2013 show center of the region \n- \ud83d\udcd0 **Surface area** \u2013 compute region surface \n- \ud83d\udccf **Perimeter** \u2013 measure perimeter length \n- \ud83d\udce4 **Send to table** \u2013 export all measurements to the table widget \n- \u2795 **Add to interpolation** \u2013 add the current slice to slice-to-slice interpolation \n- \u25b6\ufe0f **Apply interpolation** \u2013 apply interpolation using current and previous slices \n\n<p align=\"center\">\n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tools_seg.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p>\n\n\n## \ud83d\udd00 Interpolation between slices\nTo interpolate across slices:\n1. \u2705 Activate the colors you want to interpolate \n2. \ud83d\uddbc Select a segmented region in one plane (sagittal, axial, or coronal) \n3. \u2795 Add more regions from other slices (as many as needed) \n4. \ud83d\uddb1 Right-click \u2192 **Apply interpolation** \n5. \u23f3 Wait for interpolation results \n\n\n\n## \ud83d\udccf Ruler\nThe ruler measures distances between two points in an image. \nRight-click on a ruler gives access to:\n- \ud83c\udfaf **Center position** \n- \ud83d\udccf **Length** \n- \ud83d\udcd0 **Line angle** \n- \ud83d\uddd1 **Remove** \u2013 delete the current ruler \n- \ud83d\udce4 **Send to table** \u2013 export ruler data \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/additional_resources/tools_ruler.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p>\n\n\ud83d\udd04 You can add unlimited rulers.\n\n\n\n## \ud83e\uddf0 Tools menu\nOptions available under the **Tools menu**:\n\n- \u21a9\ufe0f **Undo** \u2013 revert up to 10 segmentations \n- \u21aa\ufe0f **Redo** \u2013 redo up to 10 actions \n- \ud83e\uddea **Preprocessing** \u2013 N4 Bias Field Correction, Image Masking, BET, DeepBET, Thresholding, Masking Ops, Change CS \n- \u2139\ufe0f **Basic Info** \u2013 Histogram, Resize, Image Info \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_tools.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p>\n\n### \ud83e\uddee N4 Bias Field Correction\nUses SimpleITK. Parameters include:\n- Otsu thresholding for mask creation \n- Fitting level \n- Shrinking factor \n- Max iterations \n- Image selection (top = first image, bottom = second image) \n\nAfter running, you can restore the **Original** image if needed.\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_n4b.png\" alt=\"MELAGE\" width=\"600\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n\n### \ud83c\udfad Image Masking\nKeep or remove image parts using segmentation masks:\n- Image selection (top or bottom) \n- Action: **Keep** / **Remove** \n- Mask color \n- Apply button \n\nReset by using mask color `9876_Combined`.\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_masking.png\" alt=\"MELAGE\" width=\"600\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n\n\n### \ud83e\udde0 Brain Extraction Tool (BET)\nImplements [Smith 2002](https://pubmed.ncbi.nlm.nih.gov/12391568/). \nParameters:\n- Advanced mode \n- Iterations \n- Adaptive thresholding \n- Fractional threshold \n- Search distance \n- Radius of curvature \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_bet.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n\n\n### \ud83e\udd16 Deep Learning Brain Extraction\nDL-based brain extraction with configurable options:\n- Advanced mode (editable) \n- Image selection \n- Model selection \n- CUDA acceleration (optional) \n- Threshold (-4 to 4) \n- Network weights path \n- Apply button \n\n\ud83d\udca1 Tip: Adjust threshold without rerunning the model.\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_deepbet.png\" alt=\"MELAGE\" width=\"600\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p>\n\n\n### \u2696\ufe0f Image Thresholding\nMulti-Otsu based thresholding:\n- Image selection \n- Number of classes \n- Apply \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_threshold.png\" alt=\"MELAGE\" width=\"600\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p>\n\n\n### \u2795\u2796 Masking Operations\nCombine masks using summation or subtraction:\n- Masking color(s) \n- Operation \n- Image selection \n- Apply \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_maskO.png\" alt=\"MELAGE\" width=\"600\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n\n\n### \ud83e\udded Change CS (Coordinate System)\n- Image selection \n- From (current system) \n- To (desired system) \n- Apply \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_cs.png\" alt=\"MELAGE\" width=\"600\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n\n\n### \ud83d\udcca Basic Info\nTools for inspecting and resizing images.\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_basic.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n- \ud83d\udcc8 **Histogram** \u2013 view image histogram \n- \ud83d\udcd0 **Resize** \u2013 isotropic resize \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_resize.png\" alt=\"MELAGE\" width=\"400\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n- \u2139\ufe0f **Image info** \u2013 metadata with search \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/tools_imageinfo.png\" alt=\"MELAGE\" width=\"500\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n\n\n# \ud83d\udcc2 File Menu\n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file.png\" alt=\"MELAGE\" width=\"500\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\nOptions include:\n- \ud83c\udd95 **New project** \u2013 start fresh \n- \ud83d\udcc2 **Load project** \u2013 open saved project \n- \ud83d\udcbe **Save** \u2013 overwrite project \n- \ud83d\udcbe **Save as** \u2013 save under new name \n- \ud83d\udce5 **Import** \u2013 import segmentation \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_import.png\" alt=\"MELAGE\" width=\"500\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n- \ud83d\udce4 **Export** \u2013 save modified image/segmentation with suffix \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_export.png\" alt=\"MELAGE\" width=\"500\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n- \ud83d\udcf8 **Screenshot** \u2013 capture a plane or whole scene \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_ss.png\" alt=\"MELAGE\" width=\"500\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n- \u274c **Close top image** \u2013 close first (top) image \n- \u274c **Close bottom image** \u2013 close second (bottom) image \n- \u2699\ufe0f **Settings** \u2013 change application defaults \n\n<p align=\"center\"> \n<img src=\"https://raw.githubusercontent.com/BahramJafrasteh/MELAGE/main/resource/manual_images/menu_file_settings.png\" alt=\"MELAGE\" width=\"500\" style=\"border:1px solid black\" object-fit=\"contain\"/>\n</p> \n\n- \ud83d\udeaa **Exit** \u2013 close app (confirmation window will ask to save project)\n\n# \ud83d\udcdc License \nFor licensing inquiries, please contact: \n- [b.jafrasteh@gmail.com](mailto:b.jafrasteh@gmail.com) \n- [baj4003@med.cornell.edu](mailto:baj4003@med.cornell.edu) \n\n## Protection & Registration \n**MELAGE** is registered in the **Electronic Register of Intellectual Property** as software, under file **FCAD-22002**, by the Technology Transfer Office of the Andalusian Public Health System (OTT-SSPA). \n- **Identifier:** 2211222681375 \n- [View registration details on SafeCreative](https://www.safecreative.org/work/2211222681375-melage?0) \nThis legal protection ensures intellectual property rights are formally secured.\n\n\n# \ud83d\udcd6 Citation & Acknowledgements \nIf you use **MELAGE** in your research, please cite the following work: \n\n> Jafrasteh, B., Lubi\u00e1n-L\u00f3pez, S. P., & Benavente-Fern\u00e1ndez, I. (2023). \n> *MELAGE: A purely Python-based Neuroimaging Software (Neonatal).* \n> arXiv preprint arXiv:2309.07175 \n\nWe would like to acknowledge all contributors and collaborators who have supported the development and testing of MELAGE. \n\n\n\n# \ud83d\ude80 Releases \nStable releases and updates of **MELAGE** are available on the [GitHub Releases page](https://github.com/BahramJafrasteh/MELAGE/releases). \n- \ud83d\udfe2 **Stable releases**: Fully tested, recommended for production and research use. \n- \ud83e\uddea **Pre-releases / beta versions**: For testing new features and providing feedback. \n\nStay updated by watching the repository for new release notifications.\n",
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