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MIB specifications


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




No version available



  • person_outline Eija Jokitalo

Additional information


Publication for Microscopy Image Browser

MIB citations


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

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

[…] MOS (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 fluores […]


Cytoskeletal Stability in the Auditory Organ In Vivo: RhoA Is Dispensable for Wound Healing but Essential for Hair Cell Development

PMCID: 5602105
PMID: 28929130
DOI: 10.1523/ENEURO.0149-17.2017

[…] EG scanning electron microscope equipped with a 3View system (Gatan). The cutting z-step was 40 nm. Specimens were imaged with the final pixel size of 20 nm. Obtained images were further processed in Microscopy Image Browser (). 3D representations of data were segmented using Amira (Visage Imaging) and Microscopy Image Browser and further rendered in Amira. […]


Dynamics of in vivo ASC speck formation

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

[…] ransformation, 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). […]


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

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

[…] ging 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). […]


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

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

[…] -SEM 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 segmente […]


FYCO1 and autophagy control the integrity of the haploid male germ cell specific RNP granules

PMCID: 5324852
PMID: 27929729
DOI: 10.1080/15548627.2016.1261319

[…] of 11.5 k providing a 2X binned pixel size of 1.94 nm. IMOD software (http://bio3d.colorado.edu/imod) was used to align the tilt series, and create 3D reconstructions. The images were segmented using Microscopy Image Browser, developed by the Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki. 3D rendering of selected cytoplasmic vesicles was performed with BioimageXD ver […]


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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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