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.
A video shows the work-flow of AuTom.
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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) ICON-MICv1.0.zip (下载15)
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. ET-SPEC.zip (下载32) The source code of ET-SPEC is available. sourcecode.zip (下载30)
A Tutorial on getting started with ET-SPEC. Make sure you have installed softwareforET-SPEC.zip (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 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 BBa.st -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