Q&A page allows you to submit questions about our programs and exchange ideas with others.
AuTom-dualx is a toolkit for fully automatic alignment of dual-axis tilt series with simultaneous reconstruction. Here we give out the pre-compiled exe and test datasets as well as their anticipated results:
dualxmauto(pre-compiled exe): dualxmauto_ubuntu (3 downloads)
volrec_mltm_ubuntu (2 downloads)
volrec_mtlm(source code): volrec_mtlm.tar.gz (3 downloads)
Here are the examples demonstrated in the manuscript “Dualxmauto: a toolkit for fully automatic alignment of dual-axis tilt series with simultaneous reconstruction”.To run the examples, module dualxmauto and volrec_mltm is needed.If you extract the tar of testdata, a cmd.txt can be found. Following the cmd.txt you can get the result as in the manuscript or _Anticipated_result.
tools: tools.tar.gz (2 downloads)
markerauto 1.6.3 version
If the reader run as “markerauto -i V4B_G1_Tilt2.mrc -a V4B_G1_Tilt2.rawtlt -d -1 -o V4B_G1_Tilt2.xf -n V4B_G1_Tilt2.tlt”, markerauto1.6+ will use the old fasion to process the data. If the reader run as “markerauto -i V4B_G1_Tilt2.mrc -a V4B_G1_Tilt2.rawtlt -d -1 -o V4B_G1_Tilt2.xf -n V4B_G1_Tilt2.tlt -t”, markerauto1.6+ will use the Gaussian mixture model based fiducial marker tracking to process the data, which is much fater than the old fashion. The “-t” mode will use GMM-based model and the old fashion will use RANSAC-based model, users can make a execution comparion between these two model. However, because GMM-based model is in its first stage, it is still not so robust. Users are advised that use RANSAC-based model as default and use GMM-model for large field dataset.
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. Currently, the markerbasd alignment and reconstruction of AuTom is the mostly well challenged module, while the markerfree alignment still has the limitations of data features. 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 installation guide to learn how to install Autom. You need to 1.download software package of AuTom. 2.Install Library dependencies listed in installation guide: CUDA8, mpich2-1.4.1, gnuplot-5.0.5, libgd-2.1.0 and other dependencies. 3.Click Autom or type “./Autom” in terminal to run the Program. The tutorial and videos (markerbased_video, markerfree_video) show you how to use Autom step by step. Apart from the user iterface, you can also access the modules in the terminal. Please read the user-guides inside the doc package.
7.A few bug fixes.
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 (108 downloads) ICON-GPU_v1.2.5_Ubuntu64.tar.gz ICON-GPU_UserGuide_v1.2.5.pdf (61 downloads) ICON-MICv1.0.zip (61 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. ET-SPEC.zip (118 downloads) The source code of ET-SPEC is available. sourcecode.zip (42 downloads) A Tutorial on getting started with ET-SPEC. Make sure you have installed softwareforET-SPEC.zip (110 downloads) . Dual-axis nowarp,marker,projection,tracking result generated by ET-SPEC. test_mean_nowarp.tar.gz (109 downloads) Dual-axis warp,marker,projection,tracking result generated by ET-SPEC. test_mean_warp.tar.gz (103 downloads)
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 (82 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 (150 downloads) material_data_1.tar.gz (153 downloads) http://v.youku.com/v_show/id_XMTM0ODExMDgyOA==.html
atomalign alpha version
Marker_free alignment module. Material data contains the exe; Mitochondria contains a test data (with 2048×2048 size).
mitochondria.tar.gz (127 downloads)
material data2.tar.gz (95 downloads)
http://v.youku.com/v_show/id_XMTM0ODExMDY2NA==.html dualxmauto_ubuntu (3 downloads) dualxmauto_ubuntu (3 downloads) tools.tar.gz (2 downloads) tools.tar.gz (2 downloads)