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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


No version available


  • person_outline Albert Cardona
  • person_outline Albert Cardona

Additional information

Publication for TrakEM2

TrakEM2 citations


Synaptic Spinules in the Olfactory Circuit of Drosophila melanogaster

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 to their morp […]


A Phenotyping Method of Giant Cells from Root Knot Nematode Feeding Sites by Confocal Microscopy Highlights a Role for CHITINASE LIKE 1 in Arabidopsis

Int J Mol Sci
PMCID: 5855651
PMID: 29389847
DOI: 10.3390/ijms19020429
call_split See protocol

[…] ed by all the GCs (normally 5–8) in the ten sections where they showed a maximum enlargement, was measured from five independent galls per line by using the ImageJ ( plugin TrakEM2 [,]. The average size area and standard error for each value were calculated. For statistical analysis, a Student’s t-test was performed (p < 0.05). […]


Small scale screening of anticancer drugs acting specifically on neural stem/progenitor cells derived from human induced pluripotent stem cells using a time course cytotoxicity test

PMCID: 5756610
PMID: 29312819
DOI: 10.7717/peerj.4187
call_split See protocol

[…] on days 1, 2, 3, and 7 to monitor neurospheres in the microwells ( and ), and the projected areas of neurospheres () were measured using a pen tablet (Intuos, CTH-480; Wacom, Saitama, Japan) with the TrakEM2 plugin () in ImageJ (Fiji package) (; ). Microwells containing multiple neurospheres on day 0 were excluded from analysis. Outliers in a boxplot of neurosphere sizes on day 0 were also exclude […]


3D MALDI Mass Spectrometry Imaging of a Single Cell: Spatial Mapping of Lipids in the Embryonic Development of Zebrafish

Sci Rep
PMCID: 5668422
PMID: 29097697
DOI: 10.1038/s41598-017-14949-x

[…] iple, stacked MALDI-MS images. First, 2D profile images of each specific m/z were produced using ImageQuest and saved in ‘.TIFF’ format; then, all the images were stacked together as a 3D model using TrakEM2 module– of ImageJ (; version 1.50e). Each 2D image was placed on top of the previous image, and adjusted for x, y position and rotation to properly orient the section […]


Three dimensional image reconstruction of distribution of Pnmt+ cell derived cells in murine heart

Sci Data
PMCID: 5613735
PMID: 28949324
DOI: 10.1038/sdata.2017.134
call_split See protocol

[…] n, a non-rigid image registration method, was implemented by Csepe et al.. Similar to our study, Osuala et al. applied rigid registration in aligning the slices of the heart. The open source software TrakEM2 presented by Cardona et al. is a valuable platform for image volume composition from 2D histological images and provides key functionalities such as data management and semi-automatic/automati […]


Biomechanical properties of predator induced body armour in the freshwater crustacean Daphnia

Sci Rep
PMCID: 5575280
PMID: 28851950
DOI: 10.1038/s41598-017-09649-5

[…] the emission filter set to 568 nm. Due to its size D. longicephala had to be scanned in multiple image stacks for each individual. These stacks were stitched before analysis, using the ImageJ plugin TrakEM2. […]


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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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