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 is built on top of EMAN and EMAN2. Publication|Software

  2. s2stigmator: real-time detection and single-pass minimization of TEM objective lens astigmatism. Publication|Software

  3. 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. Publication|Available in jspr

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

  5. FitCTF2: determination of CTF parameters using 3 different methods (s1psfit, s2psfit, s2focus) for cross-validation. Publication|Software|Also available in jspr

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

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

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

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

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

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

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

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

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