Search Results for "3d reconstruction"
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Showing 59 open source projects for "3d reconstruction"
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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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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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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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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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We design our technology to make workforce management easier. APS offers core HR, payroll, benefits administration, attendance, recruiting, employee onboarding, and more.
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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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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... -
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LorDG
3D genome reconstruction with Lorentzian objective function
LorDG is a software to build 3D chromosomes and genome model from chromosomal contact data such as Hi-C, TCC, 5C. Detail on how to use it: https://github.com/BDM-Lab/Lordg It is published in Nucleic Acids Research : http://nar.oxfordjournals.org/content/early/2016/11/29/nar.gkw1155.long Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory, Jianlin Cheng, PhD Department of Computer Science University of Missouri, Columbia Email: chengji@missouri.edu -
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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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Cybervision - 3D reconstruction software
Cybervision is a 3D reconstruction software for SEM images
Project has moved Github at https://github.com/zlogic/cybervision Cybervision is a 3D reconstruction software for SEM images. It's an abandoned project, but can be useful as a working example for many, many technologies, such as: * Qt (including threads, vectors, graphics and OpenGL) * Eigen library (http://eigen.tuxfamily.org/) * libsift library (https://sourceforge.net/projects/libsift/) * OpenCL and of course, 3D reconstruction in general. -
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types... -
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3D surface reconstruction has been proposed as a technique by which an object in the real world can be reconstructed from a set of only 2D digital images. This rubric is very useful in many applications including robot navigation, terrain modeling, remote surgery, shape analysis, computer interaction, scientific visualization, movie making, and computer aided design. In this work, we studied photometric stereo approach as a single view 3D reconstruction technique, performed experimental...
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Canopy Reconstruction
Software for the reconstruction of plants using multiple camera views
This software reconstructs 3D plant models in multiple views. Point cloud input is segmented, then patches of leaf surface are grown using the level set method. Please see the CPIB website for news of updates and further development.