Q&A page allows you to submit questions about our programs and exchange ideas with others.
Related materials of “Live-cell single molecule-guided Bayesian localization super-resolution microscopy”
Related materials of “Live-cell single molecule-guided Bayesian localization super-resolution microscopy”. These datasets includes two actin structure and one Endoplasmic reticulum structure.
These datasets are owned by Professor Pingyong Xu’s group, and any people who want to use these data should cite the paper “Live-cell single molecule-guided Bayesian localization super-resolution microscopy” and “Rational design of true monomeric and bright photoactivatable fluorescent proteins”. For further information, please contact email@example.com, firstname.lastname@example.org.
AuTom-dualx is a toolkit for fully automatic alignment of dual-axis tilt series with simultaneous reconstruction. It provides global consistent alignment with projection model with different complexity. The default alignment is based on the distortion correction along x, y and z direct. The users are recommended to use this model but a high-level distortion correction is also available by option “-w 2”. Here we give out the pre-compiled exe and test datasets as well as their anticipated results:
volrec_mltm_ubuntu14 (91 downloads)
volrec_mltm(source code): volrec_mtlm.tar.gz (90 downloads) This code has been compiled and run with open MPI 1.8.3 version successfully
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 (82 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.
program: markerauto_Centos6.5.tar.gz (199 downloads) , markerauto_RedHatEnterprise6.4.tar.gz (169 downloads) , markerauto_Ubuntu14.tar.gz (106 downloads) , markerauto_Ubuntu16.04.tar.gz (166 downloads)
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_v1.2.8_CentOS64.tar (9 downloads) ICON-GPU_v1.2.8_Ubuntu64.tar (7 downloads) ICON-GPU-v1.2.8_UserGuide.pdf (7 downloads) ICON-MICv1.0.zip (134 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 (197 downloads) The source code of ET-SPEC is available. sourcecode.zip (122 downloads) A Tutorial on getting started with ET-SPEC. Make sure you have installed softwareforET-SPEC.zip (176 downloads) . Dual-axis nowarp,marker,projection,tracking result generated by ET-SPEC. test_mean_nowarp.tar.gz (294 downloads) test_mean_nowarp_rot90.tar.gz (71 downloads) Dual-axis warp,marker,projection,tracking result generated by ET-SPEC. test_mean_warp.tar.gz (276 downloads) test_mean_warp_rot90.tar.gz (69 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 (155 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 (375 downloads) material_data_1.tar.gz (221 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 (207 downloads)
material data2.tar.gz (169 downloads)