Our research involves development of computer programs that are used in all stages of cryo-EM image processing and 3-D reconstruction. The following programs are distributed for free academic use. Note that some of these programs are no longer further maintained.

Software Developed at Purdue

  1. jspr: software for single particle cryo-EM image processing and 3-D reconstruction. It includes individual programs (2-11) listed below. It is built on top of EMAN and EMAN2. Publication

  2. DiaGrid: Single Particle Cryo-EM 3-D Reconstruction: online version of jspr. User Guide

  3. FitCTF2: determination of CTF parameters using 3 different methods (s1psfit, s2psfit, s2focu) for cross-validation. Publication|Software

  4. ctffind.py: Python script that runs ctffind3 program in parallel for large number of micrographs in batch mode

  5. j3dr: 3-D reconstruction program parallelized using EMAN2 library and MPI. Available in jspr

  6. nikontiff2mrc: convert TIFF output image by Nikon SuperCool Scanner to MRC format and convert the pixel values from transmittance to o.d.

  7. Asymmetric Reconstruction: 3-D reconstruction of complex systems with symmetry mismatches. Download. Original version as part of EMAN software

  8. MaskGold and SimGold: Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components. Publication|Software

  9. Motion Correction: UCSF MotionCorr enhanced with rolling window average, internal vertical flip, and support of more image formats. Software

  10. tomoAlign: A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law. Publication|Software

  11. tomoThickness: Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law. Publication|Software

  12. AstigmatismPlot: a Gatan Digital Micrograph plugin that plots live FFT radial profile along multiple directions. More sensitive detection of residual astigmatism than monitoring the "roundness" of live FFT. Software

  13. Elliptic distortion estimation and correction: determine the distortion parameters directly from particle images as part of 2-D alignment without the need of pre-calibration of the microscope. Available in jspr|Publication

  14. s2stigmator: real-time detection and single-pass minimization of TEM objective lens astigmatism. Publication|Software (coming soon)

Software Developed at NCMI

  1. FitCTF: automated fitting of contrast transfer function parameters using complete EMAN ctf model. Publication|Download

  2. Icosahedral Virus Reconstruction in EMAN: improved supports for 2-D alignments and 3-D reconstruction of large icosahedral viruses. Distributed as part of EMAN software

  3. MPSA: improved cross common line method for 2-D alignment of icosahedral viruses. Distributed as part of EMAN software

  4. FRM2D: 2-D alignment with fast rotation matching method. Distributed as part of EMAN software

  5. Bilateral Filter: edge-preserving method for denoising 2-D images and 3-D maps. Distributed as part of EMAN software

  6. SAVR: semi-automated virus reconstruction using common lines and Fourier Bessel reconstruction. Publication|Download

  7. Helixhunter: identify helices in density maps at subnanometer resolutions and search for homologous protein folds. Distributed as part of EMAN software

  8. Foldhunter: automated fitting density maps. Distributed as part of EMAN software

  9. Web CTF : Web based simulation of contrast transfer function and evelope functions. Publication