| ToolName | Link | License | Importance | Description | Category | Python? | Matlab? | R? | C/C++? | OtherLanguage? | VersionToStartWith | SupportedOS | MostImportantUserInterfaceStyle | Dependencies | Visualization |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NionSwift | https://nionswift.readthedocs.io/en/stable/#who-uses-nion-swift | Open | 1 | Instrument control and analysis tool for Nion microscopes and others | Acquisition, Analysis | x | v0.15.7 | Win,Linux, Mac? | GUI, CLI? | none for now, but maybe future extensions need inspection of src again | 2D images, interactive, 3D ? | ||||
| TSL/OIM/OIM Analysis | https://www.edax.com/products/ebsd | Proprietary | 1 | EDAX/AMETEK EBSD software | Acquisition, Analysis | ? | v8 | Win | GUI | dongle | Primarily 2D images, some 3D rendering | ||||
| AZtechHKL | https://nano.oxinst.com/products/aztec/aztechkl | Proprietary | 1 | Oxford instrument EBSD software | Acquisition, Analysis | ? | ? | Win | GUI | dongle | Primarily 2D images, some 3D rendering | ||||
| ESPRIT | https://www.bruker.com/de/products-and-solutions/elemental-analyzers/eds-wds-ebsd-SEM-Micro-XRF/software-esprit-family.html | Proprietary | 1 | Bruker EBSD software | Acquisition, Analysis | ? | ? | Win | GUI | dongle | Primarily 2D images, some 3D rendering | ||||
| DREAM.3D | http://dream3d.bluequartz.net/ | Open | 1 | Tool for creating discretized RVE for computational materials science and EBSD 3D reconstruction | Analysis | x | x | v6.5.510 | Win,Linux,Mac? | GUI, CLI | HDF5, Java | 2D graphs, 3D voxel structured grid data via HDF5/XDMF | |||
| MTex | https://mtex-toolbox.github.io/ | Open | 1 | Matlab texture toolbox by Ralf Hielscher’s group | Analysis | x | v5.7 | Win,Linux,Mac | Scripting, GUI | those which come with Matlab | Matlab-based visualization | ||||
| List of software tools for cryo-EM | https://github.com/kuixu/awesome-cryoem | Open | 4 | Just for our decision making process more details | Software list, documentation | x | n/a | n/a | n/a | n/a | |||||
| abTEM | https://github.com/jacobjma/abTEM | Open | 1 | ab-initio multi-slice/PRISM STEM simulations | Physics-based image simulation | x | 6ed0b6deef3f6111c2a16cba2308373d72e6fe72 | Win?,Linux,Mac? | Scripting, GUI? | GPAW ab-initio, needs further inspection of src | 2D graphs and 3D visualization via Python/Jupyter | ||||
| hyperspy | https://hyperspy.org/ | Open | 1 | multi-dimensional data analysis | Analysis | x | v1.6.4 | Win,Linux,Mac? | Scripting | so-called HyperspyBundle package, a modified anaconda? | 2D images,graphs (interactive?) via Python/Jupyter | ||||
| LiberTEM | https://libertem.github.io/LiberTEM/ | Open | 1 | high-throughput distributed pixellated STEM analysis | Analysis | x | >=v0.8 | Win,Linux,Mac? | Scripting | self-contained | 2D images,graphs via Python/Jupyter | ||||
| imageJ | https://imagej.nih.gov/ij/index.html | Open | 1 | generic image stack processing and analyses | Analysis | Java | v1.53 | Win,Linux,Mac | GUI | self-contained, java | 2D images, 3D image stacks, rendering | ||||
| Thomas Aarholt’s list of software tools for STEM simulations | https://github.com/thomasaarholt/STEMSimulation | Open | 4 | Just for our decision making process more details | Software list, documentation | x | n/a | n/a | n/a | n/a | |||||
| EMsoft | https://github.com/EMsoft-org/EMsoft | Open | 1 | Mark de Graeff’s collection of analysis and visualization tools for electron microscopy, mainly for data acquired in SEMs, | Analysis | x | Fortran | >=v5.0 | Win,Mac | GUI | GPU mandatory? | 2D images,graphs, 3D ? | |||
| Stabix | https://github.com/stabix/stabix | Open | 1 | Slip transfer analysis toolbox with GUI, crystal plasticity tool | Analysis | x | b02b035131c873c7da30ddcc09a4c3b56b3c0d01 | Win,Linux,Mac | GUI, Scripting | those which come with Matlab | Matlab-based visualization | ||||
| ESPRIT QUBE | https://www.bruker.com/de/products-and-solutions/elemental-analyzers/eds-wds-ebsd-SEM-Micro-XRF/esprit-qube-software.html | Proprietary | 2 | Bruker EBSD software for 3D reconstruction aka Konijnenberg tool | Analysis | ? | ? | Win | GUI | dongle ? | Primarily 2D images, some 3D rendering | ||||
| Neper | https://neper.info/ | Open | 2 | Tool for creating discretized RVE for computational materials science | Analysis | x | v4.2 | Linux | CLI | FEPX ? | ? | ||||
| APEX | https://www.edax.com/products/ebsd/apex-software-for-ebsd | Proprietary | 2 | EDAX EBSD software | Acquisition, Analysis | ? | ? | Win | GUI | dongle ? | Primarily 2D images, some 3D rendering | ||||
| pyQSTEM/QSTEM | https://github.com/jacobjma/PyQSTEM | Open | 2 | (S)TEM simulations | Physics-based image simulation | x | x | n/a | n/a | n/a | no longer maintained, developer asks to use abTEM instead | n/a | |||
| prism-em | https://prism-em.com | Open | 2 | ab-initio multi-slice/PRISM STEM simulations | Physics-based image simulation | x | v1.2 | Linux | CLI, GUI for Win,Mac | need to check documentation | primarily 2D graphs | ||||
| pyxem | https://pyxem.github.io/pyxem-website/ | Open | 2 | extension of hyperspy for analyzing 4D scanning diffraction microscopy | Analysis | x | v0.12.2 | ? | Scripting | hyperspy | 2D images, graphs via Python/Jupyter | ||||
| openNCEM | https://github.com/ercius/openNCEM | Open | 2 | various EM tools of the National Center for Electron Microscopy | Analysis | x | ab0a40a1354cf7e258efd016de675d2844e7a721 | ? | Scripting | self-contained | ? | ||||
| µSTEM | https://github.com/HamishGBrown/MuSTEM | Open | 2 | Hamish Brown’s multi-slice STEM simulations | Physics-based image simulation | Fortran | b876b8346cfd173aef1c176c36bf8edfb920503b | Win | CLI | CUDA-capable GPU ? | 2D image creation | ||||
| ilastik | https://www.ilastik.org/ | Open | 2 | AI-based object segmentation and tracking | Analysis | v1.3.3 | Linux, Win, Mac ? | GUI, scriptiing | Fiji ?, need to inspect further | ||||||
| emdviewer | https://github.com/pophus/emdviewer | Open | 2 | Colin Ophus’ GUI tool to view EMD files | File format | x | c98a0e639323c3e51f714f6b9048b34b8bf87022 | ? | ? | looks unmaintained | |||||
| CSET | https://github.com/CSET-Toolbox/CSET | Open | 2 | compressed sensing 3D reconstruction SART, SIRT, FISTA | Analysis | x | ? | ? | ? | loooks unmaintained, Astra toolbox, maybe specific hardware ? | |||||
| clTEM | https://jjppeters.github.io/clTEM/guide | Open | 2 | multi-slice method STEM | Physics-based image simulation | x | v0.3.4 | Linux | CLI ? | OpenCL, GPU | 2D image creation | ||||
| AstroEBSD | https://github.com/benjaminbritton/AstroEBSD | Open | 2 | indexing tool for EBSD | Analysis | x | 443bb2dc7c0100a7ed78f13c37bed60732f7bd4a | Win | GUI, scripting | those which come with Matlab | Matlab-based visualization | ||||
| Philippe Pinard’s EBSD tools | https://github.com/ppinard/ebsdtools | Open | 2 | pieces of code which ones (should have) become an open EBSD tool | Analysis | x | 7b6104207e2512d21da0add3705a65cd57224c5a | ? | Scripting | very likely no longer maintained | n/a | ||||
| EbsdLib | https://github.com/BlueQuartzSoftware/EbsdLib | Open | 2 | BlueQuartz library for converting orientation parameterizations | Analysis | x | 3b2c842c31dedf3b1a3bfc7e5cd701b55ae7381d | ? | Library | ? | n/a | ||||
| IMOD | https://bio3d.colorado.edu/imod/ | Open | 2 | 3D visualization software | Visualization | ? | v4.11 | ? | ? | ? | 3D OpenGL | ||||
| Avizo | https://www.thermofisher.com/de/de/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software.html | Proprietary | 2 | 3D visualization software | Visualization | ? | ? | Win | GUI | dongle ? | 2D, 3D, rendering | ||||
| RELION | https://github.com/3dem/relion | Open | 3 | Regularised Likelihood optimisation | Analysis | x | x | ||||||||
| topaz | https://github.com/tbepler/topaz | Open | 3 | CNN-based particle picking | Analysis | x | |||||||||
| scipion | https://github.com/I2PC/scipion | Open | 3 | Create 3D models of macromolecular complexes | Analysis | x | |||||||||
| gala | https://github.com/janelia-flyem/gala | Open | 3 | AI-based segmentation of nD images | Analysis | x | |||||||||
| Daniel Asarnow’s tools | https://github.com/asarnow/pyem | Open | 3 | various EM tools | Analysis | x | |||||||||
| webknossos | https://github.com/scalableminds/webknossos | Open | 3 | cloud-/browser-based 3D annotation connectomics | Analysis | Java | |||||||||
| Juan Nunez-Iglesias’ tools | https://github.com/jni/ray | Open | 3 | image segmentation | Analysis | x | |||||||||
| FOCUS | https://github.com/C-CINA/focus | Open | 3 | image stack processing | Analysis | x | Fortran | ||||||||
| DragonFly | https://www.theobjects.com/dragonfly/ | Proprietary | 3 | The Object Research 2-4D image visualization and analyses | Analysis | ? | |||||||||
| Amira | https://www.thermofisher.com/de/de/home/electron-microscopy/products/software-em-3d-vis/amira-software.html | Proprietary | 3 | Thermofisher 3-4D image visualization and analyses | Analysis | ? | |||||||||
| powerfit | https://github.com/haddocking/powerfit | Proprietary | 3 | Rigid body fitting of atomic structure | Analysis | x | |||||||||
| SPIDER | https://github.com/spider-em/SPIDER | Open | 3 | system for processing image data from electron microscopy focus on single-particular reconstruction, long-standing, MRC file reader | Analysis | x | Fortran | ||||||||
| Jeffrey Ede’s tools | https://github.com/Jeffrey-Ede/partial-STEM | Open | 3 | Deep-learning GAN-type STEM tools various, Jeffrey ede has multiple repositories related to such tools | Analysis | x | |||||||||
| PyLorentz | https://github.com/PyLorentz/PyLorentz | Open | 3 | simulation and reconstructing Lorentz TEM data, magnetic induction reconstruction, TIE | Analysis | x | |||||||||
| EM-net | https://github.com/akhadangi/EM-net | Open | 3 | Deep-learning-based segmentation of EM data | Analysis | x | x | ||||||||
| ccrunch | https://github.com/hvthaibk/ccrunch | Open | 3 | reconstruction of 3D structure macromolecules GPU-based FFT correlation | Analysis | x | |||||||||
| diluvian | https://github.com/aschampion/diluvian | Open | 3 | connectomics flood filling segmentation tool | Analysis | x | |||||||||
| SBEMimage | https://github.com/SBEMimage/SBEMimage | Open | 3 | block-facet image acquisition tool for EM data, connectomics | Analysis | x | Assembler | ||||||||
| archanid | https://github.com/ezralanglois/arachnid | Open | 3 | Python-scripting interface to SPIDER | Analysis | x | |||||||||
| Nicoló Grilli’s tools | https://github.com/ngrilli/ebsd2abaqusEuler | Open | 3 | interface EBSD data with abaqus (FE mesh solver) | Parser | x | |||||||||
| MTEX2Gmsh | https://github.com/DorianDepriester/MTEX2Gmsh | Open | 3 | interface MTEX EBSD data with gmsh (general open-source FE mesher) | Parser | x | |||||||||
| pyxem/kikuchipy | https://github.com/pyxem/kikuchipy | Open | 3 | Builds on hyperspy, EBSD indexing software | Analysis | x | |||||||||
| GND | https://github.com/tskippon/GND | Open | 3 | analyses of geometrically necessary dislocation densities from EBSD | Analysis | x | |||||||||
| David Rowenhorst’S PyEBSDIndex | https://github.com/drowenhorst-nrl/PyEBSDIndex | Open | 3 | EBSD indexing hough, radon transform based | Analysis | x | |||||||||
| Steffen Brinckmann’s EBSD tools | https://github.com/SteffenBrinckmann/pythonEBSD | Open | 3 | various file parsing, orientation parameterization | Parser | x | |||||||||
| ebsd2ansys | https://github.com/frankNiessen/ebsd2ansys | Open | 3 | interface EBSD data with ansys (FE mesh solver) | Analysis | x | |||||||||
| Edward Pang’s tool for resolving pseudosymmetry | https://github.com/epang22/EBSDrefine | Open | 3 | pseudosymmetry resolving when indexing EBSD pattern | Analysis | x | |||||||||
| Frank Niessen’s tools | https://github.com/frankNiessen | Open | 3 | A couple of parser tools to convert EBSD data | Parser | x |
This repository was archived by the owner on May 2, 2023. It is now read-only.