Search Results for "tomography"
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Showing 44 open source projects for "tomography"
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TomoJ
ImageJ plugin to perform Electron Tomography
TomoJ is an ImageJ plug-in for tomographic reconstruction. It was designed for electron tomography, however any acquisition with parallel beam should work. TomoJ proposes the preprocessing and the registration of tilt-series prior to 3D reconstructions (WBP, ART, SIRT, OS-SART, compressed sensing). TomoJ is written in Java, the computations are multithreaded and reconstruction can be performed on CPU or GPU (OpenCL). registration is described in: Journal of Structural Biology: X. 2020... -
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EIDORS (electrical impedance and diffuse optical tomography reconstruction software) provides software, algorithms and reference data for image reconstruction and modelling.
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..., Durrani AK, Butsabong T, et al. (2021) OCTAVA: An open-source toolbox for quantitative analysis of optical coherence tomography angiography images. PLoS ONE 16(12): e0261052. https://doi.org/10.1371/journal.pone.0261052
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APIRL
Library and command line tools for Tomographic Image Reconstruction
APIRL (AR-PET Image Reconstruction Library) is a library with command line tools for tomographic image reconstruction in emission tomography. It was developed to provide an image reconstruction algorithm for the AR-PET (Argentine Positron Emission Tomography), a low cost PET scanner. The implemented algorithms are based on the well known iterative algorithms MLEM and OSEM. In addition, provides an image reconstruction algorithm for a tomographic gamma scanner for non-destructive assay... -
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jif3d
3D Joint Inversion Framework
jif3d is a framework for joint inversion of different types of geophysical data in 3D. It currently comprises forward solvers for first arrival traveltimes, scalar and tensor gravity data, magnetics, magnetotellurics, electrical resistivity tomography and surface waves.The framework is flexible in terms of the coupling approach between the different datasets. At the moment cross-gradient coupling, variation of information and deterministic parameter relationships are implemented. Other coupling... -
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AtomProbeLab
Matlab-based analysis of Atom Probe Data
A collection of scripts and functions for the analysis of atom probe tomography data. Currently, this includes: standard file operations, plotting mass spectra, mass spectra analysis and mass peak overlap solving. For more information see the Wiki: https://sourceforge.net/p/atomprobelab/wiki/Home/ Quick overview video: https://youtu.be/8rJHce7M5UU More in-depth video using the APT school demos live script: https://www.youtube.com/watch?v=cyrLHCzZwuw For details of the maximum likelihood... -
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APTTools
A collection of utilities for atom probe tomography analysis
A collection of command-line tools for atom probe analysis including: * Point data XML scripting language, load, transform, resize and otherwise alter point data * Radial Distribution Function analysis tools * Level-set tools for simulating shape transformations during experiments -
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DiInSo
DiInSo is orient to solve 3D direct and 2D/3D inverse problems of ERT
'Direct-Inverse Solver' (DiInSo) is an electrical resistivity tomography (ERT) software which orient to solve 3D direct and 2D/3D inverse problems on direct current (DC). X86 version of DiInSo is totally free and can be use in scientific purposes, but it also has not any guarantees, so use DiInSo at your own risk. READ CAREFULLY NEXT IMPORTANT MESSAGE NEVER use BLANKS and try to use only ENGLISH SYMBOLS in directories, filenames, paths and names of problems in program DiInSo. It is highly... -
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plastimatch
Volumetric image processing software
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). -
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3Depict
atom probe software : visualisation and data analysis
This software is designed to help users visualize and analyze 3D point clouds with an associated real value, in a fast and flexible fashion. The primary use is in Atom Probe Tomography, which is an atomic imaging technique. However the program may also be useful in other areas, such as geospatial data, lidar, etc. -
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DCT
Diffraction Contrast Tomography analysis code
Diffraction contrast tomography code base, as developed by researchers from beamline ID19 of the ESRF, Grenoble, France, and Manchester University, UK. -
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This project contains an open-source implementation of an OPT platform. The 3D-printable components are provided to built your customized sample stage. We offer our open source MATLAB software with an GUI for OPT imaging. We developed a generalized automated workflow including a two-step registration approach for correcting the center of rotation and provide accurate and high-quality 3D reconstruction. *Here we provide the raw tomography videos recorded using the zOPT hardware...
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TauFactor
MatLab App for calculating the tortuosity factor of microstructure
... transport resulting from convolutions of the flow paths through porous media. TauFactor calculates this value using an over relaxed finite-different approach. This tool provides a fast computational platform applicable to the big datasets (>10^8 voxels) typical of modern tomography, without requiring high computational power. -
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Finite Transform Library
A Library is for Finite Transforms
The Library is for Finite Transforms such as the Number Theoretic Transform (NTT) and Finite Radon Transform (FRT). Current modules include NTTW for NTTs with high resolution (microsecond) timing, basic array and imaging. The transforms are optimised for performance. -
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PyTom
http://www.sciencedirect.com/science/article/pii/S1047847711003492
PyTom is a toolbox developed for interpreting cryo electron tomography data. All steps from reconstruction, localization, alignment and classification are covered with standard and improved methods. Please sign up to our mailing list to keep up with the most recent updates and versions. -
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NICOS
Client/Server based experiment and instrument control system
Client/Server based experiment and instrument control system -
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ASTRA Tomography Toolbox
A high-performance GPU MATLAB toolbox for 2D and 3D tomography
NB: The ASTRA Tomography Toolbox is now hosted at http://www.astra-toolbox.com/ The ASTRA Tomography Toolbox is a MATLAB toolbox based on high-performance GPU primitives for 2D and 3D tomography, developed jointly by the ASTRA-Vision Lab research group at the University of Antwerp and CWI, Amsterdam. It supports 2D parallel and fan beam geometries, and 3D parallel and cone beam. All of them have highly flexible source/detector positioning. A large number of 2D and 3D algorithms... -
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cphcttoolbox
Cph CT Toolbox is a selection of Computed Tomography tools
Copenhagen Computed Tomography Toolbox is a collection of applications and libraries for flexible and efficient CT reconstruction. The toolbox apps generally take a set of projections (X-ray intensity measurements) and filter and back project them in order to recreate the image or volume that the projections represent. The project includes both mostly informative CPU implementations and highly efficient GPU implementations. Regular releases are hosted at the Python Package Index. -
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Toastpp
Forward and inverse modelling in optical tomography
Toast++ is a C++ software package for modelling light transport in scattering media using the finite element method. It allows 3D reconstruction of absorption and scattering distributions inside an object from boundary measurements of light transmission, using steady state, time domain or frequency domain information. Matlab and Python bindings exist for ease of use and fast prototyping. -
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This project, developed at UCL London, provides code for tomographic reconstruction. NiftyRec is written in C and has Python and Matlab extensions. Computationally intensive functions have a GPU accelerated version based on CUDA.
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RooTrak
Extracting root system architecture form X-ray µCT images
RooTrak is an open-source tool, developed to aid in the separation process of plant roots from the surrounding soil, in X-ray micro computed tomography (µCT) images. The tool facilitates the extraction and visualisation of plant root systems and allows the quantification of certain root system traits. -
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toastpp Slab
Solve the diffuse optical tomography (DOT) problem in a slab geometry.
Using TOAST++, the DOT problem is solved in a slab geometry. The forward solution at various detector positions is compared to the analytical solution to the diffusion equation. The analytical solution was calculated using different boundary conditions than those used by TOAST++, so the solutions are similar but not exactly the same. The code is written in MATLAB, and the steps are split into .m files. The steps are: 1. Generate slab nodes 2a. Generate mesh with tetgen 2b. Check... -
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CRAFT
Control Recon and Analysis for Tomography
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pyRAFT
Reconstruction Algorithms for Tomography (python)