Montaris-X is a free desktop ROI editor built for labs that need accurate delineation, multi-channel viewing, and clean exports without cloud lock-in or heavyweight setup.
Generic image viewers can draw masks, but they are usually not optimized for repeated ROI review across large microscopy or histology images. Montaris-X is tuned for that exact task.
Montaris-X opens the image types research teams actually work with and keeps contrast, channel, and orientation controls close to the annotation surface.
The editing model is tuned for repeated scientific delineation work rather than generic painting or image manipulation.
Montaris-X fits into labs that already rely on ImageJ, Python, or mask-based analysis without forcing a proprietary export path.
The application runs locally, keeps research images on your machine, and ships as an open-source project that teams can inspect and extend.
The product flow stays focused: load a scientific image, build ROI layers, refine structures, and export to the format your pipeline already expects.
Open fluorescence, brightfield, atlas, or section images and keep scientific display controls close to the canvas.
Create distinct ROI layers, assign readable colors, and switch tools based on the structure you need to capture.
Tighten masks, transform connected components, and compare channels without leaving the editing surface.
Ship ImageJ ROI bundles, masks, overlays, or native sessions with minimal cleanup before analysis.
Montaris-X keeps ROI work fast and focused while remaining compatible with established ImageJ workflows and common scientific image formats.
| Capability | Montaris-X | ImageJ / FIJI | QuPath | Napari |
|---|---|---|---|---|
| Purpose-built for ROI delineation | Yes | No | No | No |
| 16/32-bit TIFF support | Yes | Yes | Yes | Yes |
| Multi-channel composite viewing | Yes | Yes | Yes | Yes |
| Component-aware transform | Yes | No | No | No |
| ImageJ .roi import/export | Yes | Native | Yes | Plugin |
| Brush, polygon, and stamp tools | Yes | Partial | Partial | Partial |
| Session auto-save and recovery | Yes | No | No | No |
| Cross-platform desktop app | Yes | Yes | Yes | Yes |
| Free and open source | MIT | Public domain / GPL | GPL | BSD |
These are the questions most likely to come up when evaluating an ROI editor for scientific image annotation.
It is aimed at research teams working on microscopy, histology, atlas delineation, fluorescence imaging, and other scientific annotation workflows where ROI precision matters.
Yes. Montaris-X imports and exports ImageJ .roi files and ZIP bundles so labs can adopt it without rebuilding established ROI archives.
No. The editor runs locally on your machine, which keeps research data private and makes the workflow easier to deploy in controlled environments.
No. It is designed for scientific image review across Windows, macOS, and Linux, including large TIFF, fluorescence, and multi-channel image workflows.
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, Nicolas Martinez-Wise, Jessica Griffiths, Colin Yuan, and everyone in the Grant Lab for their contributions and feedback.
Use the installation guide for platform-specific setup, or jump straight in from PyPI if you already manage Python environments.
pip install montaris-x