Microscopy Image Browser


Click to enlarge Microscopy Image Browser is a high-performance software package for advanced image processing, segmentation and visualization of multidimentional (2D-4D) datasets.
Microscopy Image Browser is written in Matlab, but has a user friendly graphical interface that does not requre knowledge of Matlab and can be used by anybody.

List of Key Features:

  • Works as a Matlab program under Windows/Linux/MacOS Matlab, or as a standalone application (Windows 64bit);
  • Open source, no license/fee required;
  • Extendable with custom plugins;
  • Generation of multi-dimensional image stacks;
  • Alignment of 3D stacks and images within these stacks;
  • Brightness, contrast, gamma, image mode adjustments, resize, crop functions;
  • Automatic/manual image segmentation with help of filters and interpolation in XY, XZ, or YZ planes;
  • Quantification and statistics for 2D/3D objects;
  • Export of images or models to Matlab, Amira, IMOD, TIF, NRRD formats;
  • Direct 3D visualization using Matlab isosurfaces or Fiji 3D viewer;
  • Log of performed actions;
  • Customizable Undo option
  • Colorblind friendly default color modeling scheme


Rapid development of multidimensional microscopy imaging techniques during recent years has raised number of questions about effective image processing, visualization and analysis of the obtained datasets. Most universities worldwide provide access to the modern imaging techniques so that descriptive multidimensional datasets of the desired specimen can be fairly easily obtained by any researcher.

After acquisition the datasets have to be analyzed and quite often the detailed analysis is impossible without segmentation (creating of a model) of objects of interest out of the multidimensional data. It seems that the segmentation is the most time consuming part of the image analysis routine. For example, it may take up to a month to properly segment a single electron tomogram. The slowness of the process is caused by two main factors: limited variety of good software tools (even commercial ones) and good user-friendly segmentation algorithms that can be applied to facilitate the modeling. As a result, amount of collected and not properly processed data is much higher than the amount of produced results.

With development of Microscopy Image Browser (MIB) we address this problem and present a free, open-source software package, which can be used for image processing, analysis, segmentation and visualization of multidimensional datasets.

Helsinki Bioenergetics Group University of Helsinki Ilya Belevich's Home Page