CATMAID: collaborative annotation toolkit for massive amounts of image data

Abstract

Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy.

Availability: http://fly.mpi-cbg.de/catmaid.

Fig. 1.

(A) Sketch of the information flow between the three components of CATMAID: the central data server, the client-side user interface and several image servers. (B) Visualization of the multi-scale tiling of images. In the upper row, an exemplary ssTEM section is overlaid with the tiling grid at 25%, 50% and 100% scale. Below, exemplary tiles at the respective scale are shown (1–3). The location of a tile in the section and in lower scale tiles is indicated with the corresponding number. (C) The user interface in the synchronous navigation mode with an ssTEM dataset on the left and a relatively registered confocal stack on the right.