MIB protocols

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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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Documentation


Maintainer


  • person_outline Eija Jokitalo <>

Additional information


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

Publication for Microscopy Image Browser

MIB in pipeline

2016
PMCID: 5096676
PMID: 27814364
DOI: 10.1371/journal.pcbi.1005177

[…] using thresholding, watershed transform, and voronoi algorithms). supervised machine learning methods have also seen significant success in this space [–]. two notable examples are ilastik and microscopy image browser, two freely available programs that use supervised machine learning (edge and texture filters with random forest classification) to perform segmentation [, –]., our lab’s […]


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MIB in publications

 (13)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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