Introduction

Microscopy Image Browser is 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.

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 multidimentional 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

Description

Recent years witnessed a rapid development of 3D electron microscopy imaging techniques applied for the life science research. In addition to electron tomography (ET) that is effective on a subcellular level, several other alternative methods that extend the imaging up to the tissue level have been developed. Among these are new scanning electron microscopy (SEM) techniques that allow automated sequential imaging of a freshly cut block face of resin-embedded specimens using a back scatter detector. A fresh block face is created by an ultramicrotome inserted in the imaging chamber (Serial-Block Face SEM) or by focused ion beam (FIB-SEM). As a result, the amount and volumes of 3D datasets increases extensively raising a question of effective image processing and modeling. 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.