montaris-x 2.2.2

Cross-platform desktop ROI editor for microscopy, histology, and fluorescence imaging

Montaris-X

Cross-platform ROI editor for scientific microscopy images

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About

Montaris-X is a native desktop application for drawing, editing, and managing Regions of Interest (ROIs) on scientific microscopy images. It is built for researchers who need precise, pixel-level annotation of histological sections, brain atlases, fluorescence micrographs, and other large-format scientific imagery.

Why Montaris-X?

• Purpose-built for science — handles 16/32-bit TIFFs, multi-channel composites, and images with thousands of ROIs without breaking a sweat.
• ImageJ-compatible — import and export .roi / .zip files directly from ImageJ/FIJI workflows.
• No cloud, no account — runs entirely offline on your machine. Your data never leaves your computer.
• Cross-platform — native support for Windows, macOS, and Linux.

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Installation

Option 1: Download Pre-built Executable (Recommended)

Download the latest release for your platform from the Releases page:

Platform	File	Notes
Windows	montaris-x-windows.exe	Double-click to run. Signed binary.
macOS	montaris-x-macos	Run chmod +x montaris-x-macos && ./montaris-x-macos
Linux	montaris-x-linux	Run chmod +x montaris-x-linux && ./montaris-x-linux

macOS note: If macOS shows "unidentified developer", right-click the file and select Open, then click Open in the dialog.

Linux note: You may need to install EGL and D-Bus libraries: sudo apt install libegl1 libxkbcommon0 libdbus-1-3

Option 2: Install from PyPI

pip install montaris-x

Then launch:

montaris

Option 3: Install from Source

git clone https://github.com/digin1/Montaris-X.git
cd Montaris-X
pip install -e .

Then launch:

python main.py
# or
python -m montaris
# or
montaris

Optional: GPU Acceleration

Install Numba for JIT-compiled rendering on large images:

pip install montaris-x[accel]
# or, if installing from source:
pip install numba

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Features

Image Support

• Scientific formats — TIFF (8/16/32-bit, multi-channel), PNG, JPEG, BMP
• Multi-channel composites — split and view individual channels with false-color display
• Image adjustments — brightness, contrast, exposure, gamma with Smart Auto and Quick Boost
• Tiled rendering — LOD-based rendering for smooth navigation on large images
• Flip & Rotate — non-destructive horizontal flip and 90-degree rotation

ROI Editing

• Drawing tools — Brush, Eraser, Rectangle, Circle, Polygon, Stamp, Bucket Fill
• Transform & Move — scale, rotate, and reposition ROIs with connected-component awareness
• Multiple ROI layers — 20+ distinct colors with per-ROI opacity and fill modes (Solid, Outline, Both)
• Multi-selection — Ctrl+click to select and edit multiple ROIs simultaneously
• Undo/Redo — full global history plus per-layer undo
• Overlap handling — auto-overlap brush mode and fix-overlaps utility

Import / Export

• Native format — save/load ROI sets as .npz archives
• ImageJ compatible — import/export .roi files and ZIP bundles
• PNG masks — import/export binary mask images
• Composited overlay — export the ROI overlay as a single PNG
• Batch instructions — JSON/TXT instruction files for automated workflows
• Drag-and-drop — drop images and ROI ZIPs directly onto the window

Grid Canvas

• Multi-image workspace — define an NxM grid (up to 4x4) to work with multiple images side-by-side
• Independent cells — each cell has its own image, ROIs, undo history, adjustments, and downsample factor
• Click to switch — click any cell to make it the active workspace; all tools and panels follow
• Double-click to maximize — expand a single cell to fill the entire grid; double-click again to restore
• Save All — save session progress for every cell in one action (Ctrl+Alt+S)
• Export All as ZIP — export each cell's ROIs as separate ZIP files named by source image (Ctrl+Alt+E)
• Per-cell downsampling — each cell can have its own downsample factor with correct upscaling on export

Interface

• Dark & Light themes — switch between themes on the fly
• Collapsible sidebars — minimize panels for a distraction-free canvas
• Fullscreen mode — F11 for immersive editing
• Minimap — always-visible overview of the full image
• Performance monitor — real-time FPS and memory usage
• Global opacity slider — adjust overlay transparency from the toolbar
• Session save — auto-save and restore progress across sessions
• Persistent settings — Flip on Load and Rotate on Load are remembered across launches

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Keyboard Shortcuts

Click to expand full shortcut reference

File

Shortcut	Action
Ctrl+O	Open Image(s)
Ctrl+Shift+O	Load ROI Set
Ctrl+S	Save ROI Set
Ctrl+Shift+S	Save Progress (Session)
Ctrl+Alt+S	Save All Grid Sessions
Ctrl+E	Export ROI(s) as PNG
Ctrl+Alt+E	Export All Grid Cells as ZIP
Ctrl+W	Close Image(s)
Ctrl+Q	Quit

Edit

Shortcut	Action
Ctrl+Z	Undo
Ctrl+Y / Ctrl+Shift+Z	Redo
Ctrl+Alt+Z	Layer Undo
Ctrl+Alt+Y	Layer Redo
Ctrl+A	Select All ROIs
Delete	Delete Active ROI(s)

View

Shortcut	Action
Ctrl+0	Fit to Window
Ctrl+1	Reset Zoom (1:1)
Ctrl+=	Zoom In
Ctrl+-	Zoom Out
Ctrl+H	Flip Horizontal
Ctrl+R	Rotate 90 CW
Ctrl+[	Collapse Left Sidebar
Ctrl+]	Collapse Right Sidebar
Ctrl+Shift+M	Maximize / Restore Grid Cell
F11	Fullscreen
Ctrl+Shift+P	Screenshot

Tools

Shortcut	Action
H	Hand (pan)
Q	Select ROI
B	Brush
E	Eraser
P	Polygon
G	Bucket Fill
R	Rectangle
C	Circle
S	Stamp
T	Transform (selected)
Shift+T	Transform All
V	Move (selected)
Shift+V	Move All
[ / ]	Adjust brush size (adaptive steps)
Space	Pan (hold)
Enter	Finish Polygon
Escape	Cancel / Clear selection

Navigation

Shortcut	Action
Scroll wheel	Zoom in/out
Middle-click drag	Pan
Ctrl+Click	Toggle ROI selection

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Supported Formats

Type	Formats
Images	TIFF (.tif, .tiff) including 16/32-bit, PNG, JPEG, BMP
ROI Sets	NumPy Archive (.npz), ImageJ ROI (.roi), ZIP bundles, PNG masks
Instructions	JSON (.json), Text (.txt)

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Building from Source

Running Tests

pip install -e ".[test]"
pytest

Building a Standalone Executable

pip install pyinstaller
pyinstaller --name montaris-x --onefile --windowed --hidden-import montaris --collect-all montaris montaris/__main__.py

The executable will be in the dist/ folder.

Building a Python Package

pip install build
python -m build

This produces .whl and .tar.gz files in dist/ for distribution.

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System Requirements

• Python 3.10 or higher (for source/PyPI installation)
• OS: Windows 10+, macOS 11+, or Linux (X11/Wayland with EGL)
• RAM: 4 GB minimum, 8 GB+ recommended for large images
• Dependencies: PySide6, NumPy, SciPy, scikit-image, tifffile, Pillow, psutil

Linux System Dependencies

On Debian/Ubuntu, install the required Qt runtime libraries:

sudo apt install libegl1 libxkbcommon0 libdbus-1-3

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Code Signing

Code signing via SignPath.io (certificate by SignPath Foundation) has been applied for and is pending approval.

• Privacy policy: This program does not transfer any information to other networked systems unless specifically requested by the user or the person installing or operating it.

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Contributing

Contributions are welcome! Please open an issue or submit a pull request on GitHub.

1. Fork the repository
2. Create a feature branch (git checkout -b feature/my-feature)
3. Commit your changes
4. Push to the branch and open a Pull Request

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Acknowledgments

Montaris-X is developed in the Centre for Clinical Brain Sciences, University of Edinburgh, with support from the Grant Lab.

Special thanks to:

• Prof Seth Grant — Principal Investigator, Professor of Molecular Neuroscience
• Nicolas Martinez-Wise — Feature design, testing, and bug reports
• Jessica Griffiths — Feature design and testing
• Colin Yuan — Testing and feedback

And everyone in the Grant Lab for their continued feedback and support.

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License

Montaris-X is released under the MIT License.

Copyright (c) 2026 Digin Dominic and Montaris-X Contributors