MIB3 is a MATLAB application for processing, segmentation, analysis and visualisation of multidimensional (2D-4D) microscopy datasets.
It reads a wide range of microscopy formats, works with datasets larger than available memory through virtual and big-data modes, and provides manual, semi-automatic and deep-learning based segmentation tools.
- Project site and downloads: https://mib.helsinki.fi
- Developed at the University of Helsinki
- MATLAB R2025b or newer (R2026a is recommended)
- A compiled standalone version, which does not require a MATLAB licence, is distributed separately from https://mib.helsinki.fi or github releases
cd mib
mib3- User documentation:
docs/(built with Zensical), published in two versions:- current release: https://mib.helsinki.fi/help/main3/index.html
- nightly version, matching this repository: https://ajaxels.github.io/MIB3/ (updated
automatically on every push that changes
docs/html/)
- API reference:
docs_api/(built with Sphinx), published in two versions:- current release: https://mib.helsinki.fi/help/api3/index.html
- nightly version, matching this repository: https://ajaxels.github.io/MIB3/api/ (built
automatically from
docs_api/and the docblocks inmib/on every push that changes them)
- Developer notes:
development/INDEX.md
MIB is distributed under different terms depending on the form in which you use it:
| Form | Licence |
|---|---|
| MATLAB source code - this repository | GNU General Public License v3 or later |
| Compiled standalone application | Separate licence, see MIB standalone licence |
| Bundled external packages | Their own respective licences, see external licences |
The authoritative summary is at https://mib.helsinki.fi/license.html.
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see https://www.gnu.org/licenses.
Copyright (c) 2010-2026 Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen and Eija Jokitalo.
If you use MIB in your research, please cite it. See https://mib.helsinki.fi for the current citation.