AuTom beta1.0.1

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. Install guide ,tutorial ,user-guide and other documents are inside the doc package. These Videos show the work-flow of AuTom: markerbased_video, markerfree_video

AuTom beta1.0.1 updates:
1.AuTom now has CTF determination and correction function.
2.AuTom does not need IMOD modules anymore.
3.Reduce the time of reconstruction.
4.Add fast mode to alignment.
5.ICON now has geometry parameters. (For Autom, it handles them automatically, so you don’t need to concern about these parameters in Autom.)
6.ICON now includes a new option called bin, which allows you to bin down a volume. It is useful because you can see the reconstruction result sooner, especially when you want to adjust the parameters of the algorithm.
7.A few bug fixes.
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:,


AutoGDetermV1.0.rar (下载19) AutoGDetermV1.0_UserGuide.docx (下载26)

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47)   ICON-GPU_v1.2.5_Ubuntu64.tar.gz  ICON-GPU_UserGuide_v1.2.5.pdf (下载58) (下载20)


Dual-axis alignemnt and reconstruction result  processed by software dualxmauto. dualx_data.tar.gz (下载27)    dualxmauto.tar.gz (下载28)

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36) The source code of ET-SPEC is available. (下载33)

A Tutorial on getting started with ET-SPEC. Make sure you have installed (下载24) . Dual-axis nowarp,marker,projection,tracking result generated by ET-SPEC. test_mean_nowarp.tar.gz (下载33) Dual-axis warp,marker,projection,tracking result generated by ET-SPEC. test_mean_warp.tar.gz (下载33)

markerauto 1.5.3 version

markerauto_Centos 6.5.tar.gz (下载12) , markerauto_RedHat Enterprise 6.4.tar.gz (下载8) , markerauto_Ubuntu 14.04.tar.gz (下载8) , markerauto_Ubuntu16.04.tar.gz (下载9)

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78)

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44) 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42) material data2.tar.gz (下载29)


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