Search Results for "tomography reconstruction 3d"
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Showing 78 open source projects for "tomography reconstruction 3d"
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MESHROOM
3D reconstruction software
Photogrammetry is the science of making measurements from photographs. It infers the geometry of a scene from a set of unordered photographies or videos. Photography is the projection of a 3D scene onto a 2D plane, losing depth information. The goal of photogrammetry is to reverse this process. The dense modeling of the scene is the result yielded by chaining two computer vision-based pipelines, “Structure-from-Motion” (SfM) and “Multi View Stereo” (MVS). Fusion of Multi-bracketing LDR images... -
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Open3D
A modern library for 3D data processing
Open3D is an open-source library that supports rapid development of software that deals with 3D data. The Open3D frontend exposes a set of carefully selected data structures and algorithms in both C++ and Python. The backend is highly optimized and is set up for parallelization. Open3D was developed from a clean slate with a small and carefully considered set of dependencies. It can be set up on different platforms and compiled from source with minimal effort. The code is clean, consistently... -
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hloc
Visual localization made easy with hloc
.... Just download the datasets and you're reading to go! The notebook pipeline_InLoc.ipynb shows the steps for localizing with InLoc. It's much simpler since a 3D SfM model is not needed. We show in pipeline_SfM.ipynb how to run 3D reconstruction for an unordered set of images. This generates reference poses, and a nice sparse 3D model suitable for localization with the same pipeline as Aachen. -
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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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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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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, electrical resistivity tomography and surface waves. An interface for magnetotelluric modelling codes is also included. The framework is flexible in terms of the coupling approach between the different datasets. At the moment cross-gradient coupling, mututal information and deterministic parameter... -
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AlizaMS
DICOM Viewer
DICOM Viewer Development and releases: https://github.com/AlizaMedicalImaging/AlizaMS Other versions: https://www.aliza-dicom-viewer.com - CentOS 8, Red Hat Enterprise Linux 8, Fedora 28 or newer - s. Github releases or - Flathub ¹ https://flathub.org/apps/details/com.github.AlizaMedicalImaging.AlizaMS - Fedora ¹ sudo dnf install alizams [1] Incl. arm64 architecture -
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ReViSP
ReViSP, a 3D volume rendering MATLAB tool for multicellular spheroids
Reconstruction and Visualization from a Single Projection (ReViSP) tool: a 3D volume rendering method we developed to reconstruct the 3D shape of multicellular spheroids, besides estimating the volume by counting the voxels (3D pixels) fully included in the 3D surface. ReViSP is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code is freely provided. Requirements for running ReViSP from the source code: MATLAB 2020a and Image Processing Toolbox 11.1 or later... -
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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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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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OpenPose
Real-time multi-person keypoint detection library for body, face, etc.
OpenPose has represented the first real-time multi-person system to jointly detect human body, hand, facial, and foot keypoints (in total 135 keypoints) on single images. It is authored by Ginés Hidalgo, Zhe Cao, Tomas Simon, Shih-En Wei, Yaadhav Raaj, Hanbyul Joo, and Yaser Sheikh. It is maintained by Ginés Hidalgo and Yaadhav Raaj. OpenPose would not be possible without the CMU Panoptic Studio dataset. We would also like to thank all the people who has helped OpenPose in any way. 15, 18 or... -
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Multiview 3D Drawing
3D reconstruction pipeline based on general curve features
Reconstruct general 3D scenes using a curve drawing-based approach from ECCV 2016: "From Multiview Image Curves to 3D Drawings" -
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GPlates
Interactive visualization of plate tectonics.
GPlates is a plate-tectonics program. Manipulate reconstructions of geological and paleo-geographic features through geological time. Interactively visualize vector, raster and volume data. PyGPlates is the GPlates Python library. Get fine-grained access to GPlates functionality in your Python scripts. -
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OME-3DR
3D cell reconstruction and quantitative analysis based on OME data
For big OME data analysis, we integrate commonly used quantitative methods, describe our novel strategies to quantify and analyze biological markers related to the cell or organelle spatial-coordinate model, and present open-source OME-3-Dimensional Reconstruction (OME-3DR), a flexible, programmable and batch-oriented tool based on OME data, for reconstructing 3-dimensional (3D) spatial conformations and conducting further analyses, such as the identification, counting, localization... -
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Basilica-Sudak
3D reconstruction of ancient cross-shaped church in the woods
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
... determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn), an integrated database for annotating regulatory noncoding somatic mutations in human cancers by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms. -
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools... -
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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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Toolbox for handling X-ray transmission image data collected using the Xradia TXM system. We are constantly updating the code to implement other file formats as well - suggestions are welcome. Main articles: -) TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy, Journal of Synchrotron Radiation, 19, 281-287. (2012) http://scripts.iucr.org/cgi-bin/paper_yard?hf5192 -) 3D elemental sensitive imaging using transmission X-ray...
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SLAM++
high-performance nonlinear least squares solver for graph problems
SLAM++ is a minimalist implementation of incremental nonlinear least squares, containing lighting fast implementation of linear algebra on sparse block matrices. It is aimed for use in 3D reconstruction or robotics. -
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JPIV
Particle Image Velocimetry
JPIV is a platform independent, graphical stand-alone application for Particle Image Velocimetry (PIV) written in Java. PIV is an optical technique for measuring fluid flow velocities. JPIV moved to GitHub. Please visit us at: https://eguvep.github.io/jpiv/ -
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UmUTracker
A MATLAB program for 2D particle tracking or 3D DHM based tracking.
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing long video sequences acquired by either light microscopy or digital holography microscopy (DHM). Our program finds the 2D particle center position using an isosceles triangle transform and the axial position by a fast implementation of Rayleigh-Sommerfeld numerical reconstruction algorithm using a one dimensional radial intensity profile. *Updates v1.1: 2017/11/21- Bug... -
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MRiLab
A Numerical MRI Simulation Platform
The MRiLab project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MRiLab/ The MRiLab is a numerical MRI simulation package. It has been developed and optimized to simulate MR signal formation, k-space acquisition and MR image reconstruction. MRiLab provides several dedicated toolboxes to analyze RF pulse, design MR sequence, configure multiple transmitting and receiving coils, investigate magnetic field related properties and evaluate real-time imaging...