CATMAID statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CATMAID

Tool usage distribution map

This map represents all the scientific publications referring to CATMAID per scientific context
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Associated diseases


Popular tool citations

chevron_left 3D image visualization Neuron tracing Neuron tracing Data management and annotation 3D image reconstruction chevron_right
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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




No version available



  • person_outline Pavel Tomančák

Additional information

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Publication for Collaborative Annotation Toolkit for Massive Amounts of Image Data

CATMAID citations


TDat: An Efficient Platform for Processing Petabyte Scale Whole Brain Volumetric Images

Front Neural Circuits
PMCID: 5534480
PMID: 28824382
DOI: 10.3389/fncir.2017.00051

[…] st method for data reformatting, taking full advantage of computer hardware.In the study of connectomics, other tools are available for handling large-scale images, such as Ssecrett (Jeong et al., ), CATMAID (Saalfeld et al., ), Knossos (Helmstaedter et al., ), DVID (Katz, ), and The Open Connectome Project (Burns et al., ). These tools are mainly used for processing 3D electron microscopy image d […]


Conserved neural circuit structure across Drosophila larval development revealed by comparative connectomics

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

[…] moothness filter approximating an affine local transformation. The resulting aligned image stack was exported to an image tile pyramid with six scale levels for browsing and circuit reconstruction in CATMAID (; ). The L3v image stack is available at […]


Anatomy and function of an excitatory network in the visual cortex

PMCID: 4844839
PMID: 27018655
DOI: 10.1038/nature17192
call_split See protocol

[…] ions (< 50 nm thick) were cut and imaged spanning a 450 × 450 × 150 μm volume at 4 × 4 × 40 nm/voxel resolution. Sections representing the middle third of the EM volume were aligned and imported into CATMAID for distributed, online, manual reconstruction and targeted volumes around identified synapses were exported for volumetric segmentation and PSD analysis. EM reconstructed neurons were identif […]


Quantitative neuroanatomy for connectomics in Drosophila

PMCID: 4811773
PMID: 26990779
DOI: 10.7554/eLife.12059.032

[…] We rewrote and greatly developed the Collaborative Annotation Toolkit for Massive Amounts of Image Data, CATMAID () (GPL), to implement our methods for neural circuit reconstruction, visualization and analysis, and with a user and group […]


Object based representation and analysis of light and electron microscopic volume data using Blender

BMC Bioinformatics
PMCID: 4513682
PMID: 26208945
DOI: 10.1186/s12859-015-0652-7

[…] he neuroanatomy and connectivity of the Platynereis visual circuit []. We have extended the functionality of Blender to enable the exploration of connectomes. We provide scripts to import TrakEM2 and Catmaid [] connectome datasets. We have added functionality to query connections and to map parameters of network statistics onto a 3D model. Blender supports standard file formats, enabling transfer […]


Challenges of microtome‐based serial block‐face scanning electron microscopy in neuroscience

J Microsc
PMCID: 4745002
PMID: 25907464
DOI: 10.1111/jmi.12244

[…] mal lab computer. Therefore, several labs have developed open‐source software solutions dedicated for large‐scale 3D image data such as KNOSSOS (Helmstaedter et al., ), TrakEM2 (Cardona et al., ) and CATMAID (Saalfeld et al., ). These programs use demand‐driven dynamic data loading procedures, in which only the currently viewed subvolume is loaded into memory. As the user browses through the data, […]

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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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