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TomoJ download for Linux

Free download TomoJ Linux app to run online in Ubuntu online, Fedora online or Debian online

This is the Linux app named TomoJ whose latest release can be downloaded as TomoJ_Applications-2.8.1-jar-with-dependencies.jar. It can be run online in the free hosting provider OnWorks for workstations.

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TomoJ is an ImageJ plug-in for tomographic reconstruction.
It was designed for electron tomography, however any acquisition with parallel beam should work.
TomoJ proposes the preprocessing and the registration of tilt-series prior to 3D reconstructions (WBP, ART, SIRT, OS-SART, compressed sensing).
TomoJ is written in Java, the computations are multithreaded and reconstruction can be performed on CPU or GPU (OpenCL).

registration is described in:
Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037.
BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al.

reconstruction part was described in:
BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al


  • tomography
  • ImageJ
  • Tilt-series alignment
  • 3D reconstruction
  • WBP
  • ART
  • SIRT
  • compressed sensing

User interface

Java Swing

Programming Language

Java, OpenCL



This is an application that can also be fetched from https://sourceforge.net/projects/tomoj/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.