TrakEM2 protocols

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TrakEM2 specifications


Unique identifier OMICS_27137
Name TrakEM2
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Output data A neural circuit.
Output format NeuroML
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
ImageJ, Java3D
Source code URL
Maintained Yes


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  • person_outline Albert Cardona <>
  • person_outline Albert Cardona <>

Additional information

Publication for TrakEM2

TrakEM2 in pipelines

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

[…] microscope. when the tiles are stitched together to generate the final layer, the tile with the best contrast was chosen, and the contrast was applied to all other tiles on the same layer using trakem2 (built-in commands such as: "adjust images – enhance contrast layer-wise" and "adjust images – set min and max layer-wise")., h) in , are the 1-synapse edges meaningful? what is the error […]

PMCID: 5042088
PMID: 26179415
DOI: 10.1002/cne.23852

[…] were registered using multistackreg (thévenaz et al., ), a freely available plugin for fiji software. to annotate and measure features of interest we took advantage of a combination of programs: trakem2 (, a free plugin available from fiji image processing platform (, rrid:scires_000137; cardona et al., ); ilastik (; […]

PMCID: 5042088
PMID: 26179415
DOI: 10.1002/cne.23852

[…] identifies a structure's profile, which the program can use to follow the structure across an image stack to create a 3d reconstruction for proofreading. here we describe our pipeline involving both trakem2 and the semiautomatic tool., the recent technical solutions to 3d reconstructions that are making extremely detailed brain‐cell imaging available pave the way to quantitative analysis in 3d. […]

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TrakEM2 in publications

PMCID: 5874040
PMID: 29590193
DOI: 10.1371/journal.pone.0194861

[…] shapes of these two neurons. for siadl and siadr the apparent center position of the cluster was taken, with no obvious effect on the variability of the positioning., neurites were traced using the trakem2 add-on to fiji, using the semi-automatic tracing method ("pencil") with short (~5–10 pixel) steps between automatic tracing runs. when the automatic tracing method appeared to deduce […]

PMCID: 5880883
PMID: 29636666
DOI: 10.3389/fncel.2018.00086

[…] by two membranes: the evaginated membrane of the pc tightly covered by the invaginated membrane of the hc, which receives the protrusion (figure ). fib-sem-based dense reconstructions (done with the trakem2 plugin for imagej fiji; see supplementary material) make it possible to study invaginating protrusions in different types of olfactory neurons, which were distinguished according […]

PMCID: 5855651
PMID: 29389847
DOI: 10.3390/ijms19020429

[…] line (oectl1) compared to its control col-0 by combining a method developed to measure the gcs’ volume from semithin sections of embedded galls in combination with the 3d reconstruction plugin trakem2 [], but based on optical sections from confocal microscopy. this greatly simplified the tedious process of the embedding and sectioning of the galls. , hand-dissected galls induced by m. […]

PMCID: 5789869
PMID: 29382816
DOI: 10.1038/s41467-017-02768-7

[…] interest, and analyzing the neural elements found therein. we found the 1024 mb (32,000 × 32,000 pixels) size images can be aligned using fiji registration plugins (register virtual stack slices) or trakem2, but we still await new tools for automated segmentation,, for 3d reconstruction, a current workflow bottleneck., in conclusion, the cnt tape and staining protocol reported here will improve […]

PMCID: 5947172
PMID: 29333754
DOI: 10.1111/jmi.12676

[…] (fig. ). these are fiji (, amira ( and microscopy image browser, mib ( fiji, via the plugin trakem2 (cardona et al., ), is primarily an operator‐driven programme that is freely available. for a comparison of the programmes see table . amira and mib (belevich et al., ) have the capacity […]

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TrakEM2 institution(s)
Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Massachusetts Institute of Technology, Boston, MA, USA; Molecular Cell and Developmental Biology Department, University of California Los Angeles, Los Angeles, CA, USA
TrakEM2 funding source(s)
Supported by Kevan A. Martin, the Institute of Neuroinformatics, University of Zurich and ETH Zurich; and by grant NIH 1- R01 NS054814-05 and grant SNSF 31003A_132969.

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