Abstract
Recent developments in serial-section electron microscopy allow the efficient generation of very large image data sets but analyzing such data poses challenges for software tools. Here we introduce Volume Annotation and Segmentation Tool (VAST), a freely available utility program for generating and editing annotations and segmentations of large volumetric image (voxel) data sets. It provides a simple yet powerful user interface for real-time exploration and analysis of large data sets even in the Petabyte range.
Highlights
The acquisition of microscopic data is becoming ever faster and more and more automated, leading to the generation of enormous image datasets
Volume Annotation and Segmentation Tool is a light-weight and versatile tool specialized for volumetric annotation and segmentation of objects in very large image stacks
Typical applications include: Exploring very large EM and light microscopy (LM) image stacks interactively; efficient manual segmentation of arbitrary structures to generate voxel training data for automatic segmentation algorithms; and sparse volumetric tracing of objects of interest, either manually or assisted by an automatic segmentation of the volume
Summary
The acquisition of microscopic data is becoming ever faster and more and more automated, leading to the generation of enormous image datasets. A segmentation layer can contain segmented objects at different resolutions, and VAST automatically combines the information from different mip levels as the user moves and zooms through the data set This allows for voxel painting on very large image stacks. VastTools can export surface meshes of segmented objects to generic Wavefront OBJ files, which can be imported into 3D rendering applications like 3ds Max (Autodesk, Inc.; see example images in Figure 6), Blender (Blender Foundation) or Unity (Unity Technologies) It can export isosurface meshes (based on voxel brightness) which can for example be used to visualize fluorescence signals in light microscopic image stacks, and particle clouds, where a prototype 3D object (for example a small sphere representing a vesicle) is placed at the centers of all separately painted regions and the compound object is exported (3D object instancing). The features discussed here are described in more detail in VASTs user manual
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
