AutoGDeterm_beta_1.0.rar (7 downloads)

AutoGDeterm_beta_1.0-User-Guide.docx (9 downloads)


Automatic Tomography (Au-Tom) is for automatic reconstruction of electron tomography (ET), which covered the pre-processing, alignment and reconstruction of electron tomography. In our package, fiducial marker-based datasets and maker-free datasets are done with totally different subprocess. The presented package has the following characteristics: accurate alignment modules for datasets that contain substantial biological structures but free of fiducial markers;fully automatic alignment modules for datasets that have fiducial markers embedded in; a wide coverage of reconstruction methods with a new iterative reconstruction method that recovers “missing wedge” based on compressed-sensing theory; multi-platform acceleration solutions that support faster iterative algebraic reconstruction.

Autom has been built under Red Hat Enterprise 6.4, Cenots 6.5,Ubuntu 14.04 and Ubuntu 16.04. Other systems may not be supported well.
Read the install guide to learn how to install Autom. You can find the install guide inside the software package or you can also download it here. The tutorial and user-guide is inside the doc package.

software: Centos 6.5 (8 downloads) , RedHat Enterprise 6.4 (2 downloads) , Ubuntu 14.04 (1 download) , Ubuntu16.04 (4 downloads)

test data: material_data_1.tar.gz (53 downloads) material_data2.tar.gz (3 downloads)

A video shows the work-flow of AuTom.

ICONv1.6.4 & ICONMICv1.0.0

Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of sparsity of biological specimen.

ICONv1.6.4.tar.gz (38 downloads)     ICON_UserGuide_v1.6.4.docx (48 downloads) (9 downloads)


Dual-axis alignemnt and reconstruction result  processed by software dualxmauto. dualx_data.tar.gz (21 downloads)    dualxmauto.tar.gz (14 downloads)

ET-SPEC(formerly known as ETphantom)

ET-SPEC is a virtual electron microscopy molecular modeling simulation and 3D reconstruction system based on serial block face scanning electron microscope image(SBEM).The package contains installation instruction and a sample date. (23 downloads)

The source code of ET-SPEC is available. (24 downloads)

A Tutorial on getting started with ET-SPEC. Make sure you have installed (19 downloads) .

Dual-axis nowarp,marker,projection,tracking result generated by ET-SPEC. test_mean_nowarp.tar.gz (28 downloads)

Dual-axis warp,marker,projection,tracking result generated by ET-SPEC. test_mean_warp.tar.gz (30 downloads)

markerauto 1.5.3 version

markerauto_Centos 6.5.tar.gz (3 downloads) , markerauto_RedHat Enterprise 6.4.tar.gz (3 downloads) , markerauto_Ubuntu 14.04.tar.gz (2 downloads) , markerauto_Ubuntu16.04.tar.gz (4 downloads)

markerauto 1.5.0 version

1. The initial diameter value can be automatic detected, if the user set the initial input to -1, for example:markerauto -i -a BBa.rawtlt -n BBa_new.tlt -o BBa_fin.xf -d -1
2. fixed the bug when proceeding fiducial markers with large diameter.
3. fixed the bug for minimum number of fiducial markers (minimum number: six fiducial markers).

markerauto (73 downloads)

markerauto alpha version

Automatic marker_based alignment module.Material data contains the exe and two small test data (1024×1024). Test_106 contains a test data (with 2048×2048 size).

test_106.tar.gz (40 downloads)

material_data_1.tar.gz (53 downloads)

atomalign alpha version

Marker_free alignment module. Material data contains the exe; Mitochondria contains a test data (with 2048×2048 size).

mitochondria.tar.gz (35 downloads)

material data2.tar.gz (24 downloads)


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