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.
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.
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 (23 downloads)
The source code of ET-SPEC is available. sourcecode.zip (24 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 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 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 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).
atomalign alpha version
Marker_free alignment module. Material data contains the exe; Mitochondria contains a test data (with 2048×2048 size).