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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 <>

Additional information

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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, […]

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CATMAID in publications

PMCID: 5869015
PMID: 29528286
DOI: 10.7554/eLife.26016.038

[…] analysis of variance (manova) was performed with bonferroni correction, for multiple testing, followed by post-hoc t-test to determine exact p-value., em reconstruction was performed using catmaid as previously described (; ). a09l (dnb) neurons in a1 were identified during circuit reconstruction downstream class iv sensory neurons (), and were verified as 412-gal4 labeled neurons […]

PMCID: 5531833
PMID: 28508746
DOI: 10.7554/eLife.26000.040

[…] for the whole-mount in situ and immunostaining samples we generated projections using imaris 8.0.2 (bitplane, zürich)., neuron reconstruction, visualization, and synapse annotation were done in catmaid (; ) as described before (; ). the ciliomotor neurons described here include all neurons that form at least five synapses combined on any of the multiciliated cells in the whole larval body. […]

PMCID: 5662290
PMID: 29058674
DOI: 10.7554/eLife.29089.019

[…] abdominal segments of the ventral nerve cord (vnc) (). in the l3v, we manually reconstructed the six mdiv terminals (three per hemisegment) in abdominal segment a3 ( and ) using the web-based tool catmaid (; ). segment a3 was chosen due to its centrality in the l3v and lack of image artifacts or missing sections. in all cases, we reconstructed neurons as skeletons, expressing the 3d topology […]

PMCID: 5577918
DOI: 10.7554/eLife.28387.021

[…] that do not form synapses with prs, from a serial-section transmission electron microscopy (sstem) volume spanning the complete central nervous system of a drosophila first instar larva (using the collaborative annotation toolkit for massive amounts of image data (catmaid), ; ; ). in this way, we identified the complete repertoire of lon neurons and mapped the wiring diagram of the left […]

PMCID: 5747525
PMID: 29199953
DOI: 10.7554/eLife.26349.042

[…] thin sections. preparation, imaging, montage, and alignment of the dataset is described (). the cells were reconstructed, reviewed, 3d visualized, and the resulting synaptic network was analyzed in catmaid (; )., morphology and distribution of dense core vesicles and synapses in the inrgwa-dcr1 projection interneuron was reconstructed using trakem2 (; ). for comparing the morphology of cells […]

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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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