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Protocols

MIB specifications

Information


Unique identifier OMICS_26044
Name MIB
Alternative names Microscopy Image Browser, MIB2
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Fortran, MATLAB
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Eija Jokitalo <>

Additional information


http://mib.helsinki.fi/documentation.html

Publication for Microscopy Image Browser

MIB citations

 (14)
library_books

Three dimensional electron microscopy reveals changing axonal and myelin morphology along normal and partially injured optic nerves

2018
PMCID: 5838102
PMID: 29507421
DOI: 10.1038/s41598-018-22361-2

[…] mitochondria. at 5 nm/pixel resolution, mitochondria were identified as dark, electron-dense oval-shaped organelles with a diameter over 0.1 µm., axons, myelin and mitochondria were measured using microscopy image browser software (university of helsinki). 10 axons of varying diameter were randomly selected within the 50 × 50 µm field of view for segmentation and were traced from the first […]

library_books

A guide to analysis and reconstruction of serial block face scanning electron microscopy data

2018
PMCID: 5947172
PMID: 29333754
DOI: 10.1111/jmi.12676

[…] dm3 format. the data were then analysed using three different image analysis programmes (fig. ). these are fiji (http://fiji.sc/), amira (http://www.fei.com/software/amira-3d-for-life-sciences/) and microscopy image browser, mib (http://mib.helsinki.fi/). fiji, via the plugin trakem2 (cardona et al., ), is primarily an operator‐driven programme that is freely available. for a comparison […]

library_books

Myosin‐1C uses a novel phosphoinositide‐dependent pathway for nuclear localization

2018
PMCID: 5797967
PMID: 29330316
DOI: 10.15252/embr.201744296

[…] (andor) neo camera were used for the image acquisition. time‐lapse images were acquired with the frequency one image in 15 min during 14 h. further analysis of the video frames was performed with microscopy image browser software . for quantification of nuclear fluorescence recovery, background signal was subtracted from the nuclear signal and divided by background‐adjusted cytoplasmic […]

library_books

Dynamics of in vivo ASC speck formation

2017
PMCID: 5584180
PMID: 28701426
DOI: 10.1083/jcb.201703103

[…] which allowed mapping of the coordinates of the fluorescent spot of interest (red channel) and to overlay it on the electron micrograph. the tomograms were threshold-segmented with the microscopy image browser platform (), and the resulting model was loaded into the digital space of amira for visualization (fei)., the software geneious (version 6.1.7r; biomatters limited) was used […]

library_books

Reactive astrocytes function as phagocytes after brain ischemia via ABCA1 mediated pathway

2017
PMCID: 5481424
PMID: 28642575
DOI: 10.1038/s41467-017-00037-1

[…] conditions in merlin or sigma (carl zeiss) equipped with 3view (gatan). serial images obtained by imagej and fiji software plugins, and segmentation and image analyses were performed in trakem2, microscopy image browser and amira (fei visualization science group, usa)., total rna from cultured cells or tissues was extracted and isolated with nucleospin rna (macherey-nagel) in accordance […]

library_books

Phloem unloading in Arabidopsis roots is convective and regulated by the phloem pole pericycle

2017
PMCID: 5365319
PMID: 28230527
DOI: 10.7554/eLife.24125.022

[…] quanta 250 (fei, hillsboro, or), using a backscattered electron detector (gatan inc.). the block faces were sectioned at 40 nm increments. the images were initially processed and segmented using microscopy image browser, a self-developed program written under matlab environment (mathworks inc.) and available at http://mib.helsinki.fi/. a sbfsem dataset of 2100 images was subsequently […]


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MIB institution(s)
Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
MIB funding source(s)
Supported by Biocenter Finland, Biological Imaging Network, Academy of Finland (projects 131650 and 1287975) and the Integrative Life Science Doctoral Program of the University of Helsinki.

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