TEM Data Analysis Tools
AreTomo
Description
(Alignment and Reconstruction for Electron Tomography) GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
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ModulePaths for AreTomo
CisTEM
Description
GUI-based software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions. It provides a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions
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CrYOLO
Description
An application for fast and accurate cryo-EM particle picking. It’s based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system.
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CryoSPARC
Description
A state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.
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Remarks on CryoSPARC
Running CryoSPARC instance is provided per each Research Group basis on their scratch directory (/tem/scratch/GroupDir/.cryosparc). For more details, please refer to CryoSPARC
CTFFind4
Description
A new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFind3 and may give slightly improved results when processing data from detectors other than scanned photographic film.
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ModulePaths for CTFFind4
Dynamo
TBD
EMRNA
Description
A tool that performs Deep learning based automated RNA modeling from cryo-EM maps.
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EternaFold
Description
A tool that performs multitask learning to improve RNA structure prediction. Its training tasks include 1) predicting single structures, 2) maximizing the likelihood of structure probing data, and 3) predicting experimentally-measured affinities of RNA molecules to proteins and small molecules.
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GCtfFind
Description
GCtfFind is a new application that robustly estimates the contrast transfer function (CTF) of cryoET tilt series and cryoEM micrographs, essential information needed for cryoET subtomogram averaging and cryoEM single-particle reconstruction.
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IMOD
Description
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.
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IsoNet
Description
(ISOtropic reconstructioN of Electron Tomography) A tool that trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.
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MotionCor
Description
A multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.
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ModulePaths for MotionCor
PyEM
Description
A collection of Python modules and command-line utilities for electron microscopy of biological samples.
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PyTOM
Description
PyTom is a software package for the analysis of volumetric data obtained by cryo electron tomography (cryo-ET). It covers a complete pipeline of processing steps for tomogram reconstruction, localization of macromolecular complexes in tomograms, fine alignment of subtomograms extracted at these locations, and their classification.
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Relion
Description
Relion (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination. It is developed in the group of Sjors Scheres at the MRC Laboratory of Molecular Biology.
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ModulePaths for Relion
ResMap
Description
(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.
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SumMovie
Description
A tool that uses the alignment results from the software application Unblur to calculate movie frame sums.
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Topaz
Description
A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.
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ModulePaths for Topaz
Topaz for CryoSPARC
Description
A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models. This module is based on python runtime 3.6.
URL
https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz
Topaz for Picking Filaments
Description
A program with added support for filament start-end coordinate picking (new options -f, -fp and -fl in the extract command extract.py) in Topaz, for subsequent helical reconstruction in RELION.
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ModulePaths for Topaz filaments picking
Unblur
Description
A tool used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format and generates frame sums that can be used in subsequent image processing.
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