VANO: a volume-object image annotation system

Abstract

Volume-object annotation system (VANO) is a cross-platform image annotation system that enables one to conveniently visualize and annotate 3D volume objects including nuclei and cells. An application of VANO typically starts with an initial collection of objects produced by a segmentation computation. The objects can then be labeled, categorized, deleted, added, split, merged and redefined. VANO has been used to build high-resolution digital atlases of the nuclei of Caenorhabditis elegans at the L1 stage and the nuclei of Drosophila melanogaster's ventral nerve cord at the late embryonic stage.

Availability: Platform independent executables of VANO, a sample dataset, and a detailed description of both its design and usage are available at research.janelia.org/peng/proj/vano. VANO is open-source for co-development.

Fig. 1.

GUI and applications of VANO in annotating 3D C.elegans and D.melanogaster image stacks. (a) The 3D image viewer: a tri-view for the subject image (true color, upper left), a tri-view for the mask image (in pseudo-color, lower left) and control panel (right). The displayed images are confocal stacks of a C.elegans larva (data by Xiao Liu and Stuart Kim). The worm in this stack was straightened using the algorithm of Peng et al. (2008). (b) The annotation table viewer: a spreadsheet where each row is an annotation entry for an image object and each column holds a particular attribute of an object. In this example each object is a nucleus. (c) Application of VANO to annotating neuronal patterns in the brain of D.melanogaster. Left: the subject image where NC82 (red) stains synaptic density and GFP (green) stains a target set of neurons (data by Julie Simpson). Right: the mask image where each object, in a distinct pseudo-color, is a glia-delineated compartment of the brain (mask by Arnim Jenett).