Microscopy Image Browser
Introduction
Microscopy Image Browser (aka MIB) is a free, user-friendly and open-source software for segmentation of multidimensional datasets acquired with light and electron microscopy. MIB is written using Matlab language for scientific computing and provides access to a variety of image processing, image segmentation and image quantification tools.
History
The software is under active development since 2011 and was officially released in 2015 together with an accompanying article[1] in PLOS Biology.
In July 2020[2], MIB was extended with tools for automatic image segmentation using convolutional neural networks (aka DeepMIB) bringing the power of deep learning for all interested researchers in an easy to use workflow (PLOS Computational Biology[3]).
Main features
- Compatible with more than 100 various image formats (standard and custom Matlab readers, Bio-Formats library)
- Alignment of multidimensional datasets
- Image filters
- Manual, semi-automatic and automatic (convolutional neural networks) tools for image segmentation
- Shape and intensity quantification of objects
- Batch processing
- Extendable with custom plugins
- Volume and surface rendering for visualization
- Compatible with OMERO server, Fiji, Ilastik, IMOD, Amira and Imaris
Available releases
- As Matlab based open-source code available for all Matlab-compatible operating systems
- As compiled binaries for Windows, MacOS and Linux
| Original author(s) | Ilya Belevich |
|---|---|
| Developer(s) | Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen, Eija Jokitalo, University of Helsinki |
| Initial release | November 19, 2015 |
| Stable release | 2.702 (01.02.2021)
|
| Repository | https://github.com/Ajaxels/MIB2 |
| Written in | Matlab |
| Engine | |
| Operating system | Windows, MacOS, Linux |
| License | GNU General Public License, version 2 |
| Website | http://mib.helsinki.fi/ |
Search Microscopy Image Browser on Amazon.
Downloads available from MIB website or GitHub.
External links
- Main website: http://mib.helsinki.fi/
- Tutorials: http://mib.helsinki.fi/tutorials.html
- Documentation: http://mib.helsinki.fi/documentation.html
- Support site: https://forum.image.sc/tag/mib
- Youtube playlists: Microscopy Image Browser, MIB in brief
References
- ↑ Belevich, Ilya; Joensuu, Merja; Kumar, Darshan; Vihinen, Helena; Jokitalo, Eija (2016-01-04). "Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets". PLOS Biology. 14 (1): e1002340. doi:10.1371/journal.pbio.1002340. ISSN 1545-7885. PMC 4699692. PMID 26727152.
- ↑ Belevich Ilya, Jokitalo Eija (July 14, 2020). "DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation". Unknown parameter
|url-status=ignored (help) - ↑ Belevich, Ilya; Jokitalo, Eija (2021-03-02). "DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation". PLOS Computational Biology. 17 (3): e1008374. doi:10.1371/journal.pcbi.1008374. ISSN 1553-7358. PMC 7954287 Check
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