AutoGDeterm_beta_1.0.rar (下载14) AutoGDeterm_beta_1.0-User-Guide.docx (下载18)


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 (下载14) , RedHat Enterprise 6.4 (下载9) , Ubuntu 14.04 (下载9) , Ubuntu16.04 (下载12)

test data: material_data_1.tar.gz (下载64) material_data2.tar.gz (下载15)

A video shows the work-flow of AuTom.

If you have any problems or feedback, please leave a comment below or e-mail us. We really appreciate receiving your advice as soon as possible. E-mail:,

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. ICON-GPU_v1.2.5_CentOS64.tar.gz (下载44)   ICON-GPU_v1.2.5_Ubuntu64.tar.gz  ICON-GPU_UserGuide_v1.2.5.pdf (下载55) (下载15)


Dual-axis alignemnt and reconstruction result  processed by software dualxmauto. dualx_data.tar.gz (下载25)    dualxmauto.tar.gz (下载24)

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. (下载32) The source code of ET-SPEC is available. (下载30)

A Tutorial on getting started with ET-SPEC. Make sure you have installed (下载22) . Dual-axis nowarp,marker,projection,tracking result generated by ET-SPEC. test_mean_nowarp.tar.gz (下载31) Dual-axis warp,marker,projection,tracking result generated by ET-SPEC. test_mean_warp.tar.gz (下载32)

markerauto 1.5.3 version

markerauto_Centos 6.5.tar.gz (下载10) , markerauto_RedHat Enterprise 6.4.tar.gz (下载6) , markerauto_Ubuntu 14.04.tar.gz (下载5) , markerauto_Ubuntu16.04.tar.gz (下载7)

markerauto 1.5.0 version

updates: 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 (下载76)

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 (下载43) material_data_1.tar.gz (下载64)

atomalign alpha version

Marker_free alignment module. Material data contains the exe; Mitochondria contains a test data (with 2048×2048 size). mitochondria.tar.gz (下载36) material data2.tar.gz (下载25)


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