CATMAID pipeline

CATMAID specifications


Unique identifier OMICS_10143
Alternative name Collaborative Annotation Toolkit for Massive Amounts of Image Data
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript, Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Pavel Tomančák <>

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Publication for Collaborative Annotation Toolkit for Massive Amounts of Image Data

CATMAID IN pipeline

PMCID: 4749568
PMID: 26670546
DOI: 10.7554/eLife.11147.029

[…] error rate and synapse count variance when redundantly or repeatedly mapping connections between neurons? , we do not repeatedly trace the same neuron, instead we use the built-in functionality in catmaid to review neuron traces by different users. two expert neuroanatomists reviewed every neuron in the described circuit at least twice. each synapse was visited at least four times, […]

CATMAID institution(s)
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Institute of Neuroinformatics, Uni/ETH Zürich, Zürich, Switzerland; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
CATMAID funding source(s)
Supported by Swiss INCF Node, Institute of Neuroinformatics, Zürich, Switzerland; Swiss National Science Foundation, Switzerland; Albert Cardona, HHMI Janelia Research Campus, Ashburn, USA; FlyTEM Project, HHMI Janelia Research Campus, Ashburn, USA; Pavel Tomančák, MPI-CBG, Dresden, Germany.

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