Search Results for "tomography"
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Showing 28 open source projects for "tomography"
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TomoJ
ImageJ plugin to perform Electron Tomography
..."Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy." -
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...Sci Rep 14, 5979 (2024). https://doi.org/10.1038/s41598-024-53501-6 Untracht GR, Matos RS, Dikaios N, Bapir M, 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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EIDORS (electrical impedance and diffuse optical tomography reconstruction software) provides software, algorithms and reference data for image reconstruction and modelling.
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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 approaches can be added relatively easily. -
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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? -
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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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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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TauFactor
MatLab App for calculating the tortuosity factor of microstructure
...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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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. -
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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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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. -
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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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x-RAFT
Reconstruction Algorithms for Tomography (bash)
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pytomo
Tomography tool working as a YouTube crawler
Usage: start_crawl.py [-b --batch] [-u max_crawled_url] [-r max_rounds] [-l, --loop|--no-loop] [-R --related|--no-related] [-p max_per_url] [-P max_per_page] [-s {youtube, dailymotion}] [--snmp] [-t time_frame] [-n ping_packets] [-D download_time] [-S delay_between_requests] [-x, --no-log-ip] [-c, --no-centralize] [--http-proxy=http://proxy:8080] [--provider=MY_ISP] [--download-extra-dns] [-L log_level] [-f, --input_file input_file_list] [input_urls] -
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OpenRecon
OpenRecon is an open-source software library for image reconstruction.
Moved to https://bitbucket.org/bid/openrecon -
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Electrical Impedance Tomography and Impedance Spectroscopy software that I am developing for my PhD project.
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The aim of this project is to facilitate the development of open source software for the acceptance testing of commonly used PET (positron emission tomography) systems in accordance with published NEMA standards.