CATMAID: collaborative annotation toolkit for massive amounts of image data

By Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomancak. 2009

354 citations recorded by the source corpus.

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 Contact: tomancak@mpi-cbg.de

Subfields: Biophysics, Molecular Biology, Structural Biology, Evaluation & Benchmarks

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Citations in the corpus

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy (2010, methodology): “The TrakEM2 software used in this study combines all the components required for data acquisition, registration, navigation, and segmentation ([26,27]; http://www.”
Biological Imaging Software Tools (2012, background): “This strategy can also be easily realized on the web, allowing Google Maps–style browsing through massive multidimensional image volumes 36 .”
Visualization of image data from cells to organisms (2010, neutral): “Proper memory management is particularly important for online browsing applications that must minimize the amount of image data transferred between the client and the serve”
Quantitative neuroanatomy for connectomics in Drosophila (2015, methodology): “Collaborative circuit mapping We extended the web-based image data viewer CATMAID (Saalfeld et al., 2009) to enable a geographically distributed group of researchers to map neuronal circuitry.”
A connectome and analysis of the adult Drosophila central brain (2020, methodology): “When the same EM volume is used for many such efforts, as has occurred in the Drosophila larva and the full adult fly brain, this leads to an overall reconstruction that is the union of many individual efforts (Saalfeld et al., 2009).”
A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster (2017, methodology): “Reconstruction and analyses of neural circuits in the volume were conducted with the CATMAID tracing environment (Saalfeld et al., 2009).”
NeuroStorm: Accelerating Brain Science Discovery in the Cloud (2018, methodology): “DR AF T Image Sharing Tools CATMAID [9], a web-based annotation toolkit used on several large reconstruction projects, was extended to support BossDB as an image source.”