Related Research Articles
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set, typically a 3D scalar field.
A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection, and attenuation or absorption, to study the properties of organic or inorganic substances. "Fluorescence microscope" refers to any microscope that uses fluorescence to generate an image, whether it is a simple set up like an epifluorescence microscope or a more complicated design such as a confocal microscope, which uses optical sectioning to get better resolution of the fluorescence image.
OpenSceneGraph is an open-source 3D graphics application programming interface, used by application developers in fields such as visual simulation, computer games, virtual reality, scientific visualization and modeling.
Bitplane is a provider of software for 3D and 4D image analysis for the life sciences. Founded in December 1992, Bitplane operates out of three offices in Zürich, Switzerland, Belfast, United Kingdom, and South Windsor, Connecticut, United States.
OsiriX is an image processing application for the Apple MacOS operating system dedicated to DICOM images produced by equipment. OsiriX is complementary to existing viewers, in particular to nuclear medicine viewers. It can also read many other file formats: TIFF, JPEG, PDF, AVI, MPEG and QuickTime. It is fully compliant with the DICOM standard for image communication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality.
ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation. Its first version, ImageJ 1.x, is developed in the public domain, while ImageJ2 and the related projects SciJava, ImgLib2, and SCIFIO are licensed with a permissive BSD-2 license. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging to radiological image processing, multiple imaging system data comparisons to automated hematology systems. ImageJ's plugin architecture and built-in development environment has made it a popular platform for teaching image processing.
Endrov is an open-source plugin architecture aimed for image analysis and data processing. Being based on Java, it is portable and can both be run locally and as an applet. It grew out of the need for an advanced open source software that can cope with complex spatio-temporal image data, mainly obtained from microscopes in biological research. It lends much of the philosophy from ImageJ but aims to supersede it by having a more modern design.
Fiji is an open source image processing package based on ImageJ2.
Bioimage informatics is a subfield of bioinformatics and computational biology. It focuses on the use of computational techniques to analyze bioimages, especially cellular and molecular images, at large scale and high throughput. The goal is to obtain useful knowledge out of complicated and heterogeneous image and related metadata.
KNIME, the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept. A graphical user interface and use of JDBC allows assembly of nodes blending different data sources, including preprocessing, for modeling, data analysis and visualization without, or with only minimal, programming.
GIMIAS is a workflow-oriented environment focused on biomedical image computing and simulation. The open-source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology
MeVisLab is a cross-platform application framework for medical image processing and scientific visualization. It includes advanced algorithms for image registration, segmentation, and quantitative morphological and functional image analysis. An IDE for graphical programming and rapid user interface prototyping is available.
IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data. IMOD has been used across a range of scales from macromolecule structures to organelles to whole cells and can also be used for optical sections. IMOD includes tools for image reconstruction, image segmentation, 3D mesh modeling and analysis of 2D and 3D data.
Amira is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo.
Drishti is a multi-platform, open-source volume-exploration and presentation tool. Written for visualizing tomography data, electron-microscopy data and the like, it aims to ease understanding of data sets and to assist with conveying that understanding to the research community or to lay persons. From the website:
"The central idea about Drishti is that the scientists should be able to use it for exploring volumetric datasets as well as use it in presentations."
CloudCompare is a 3D point cloud processing software. It can also handle triangular meshes and calibrated images.
Light sheet fluorescence microscopy (LSFM) is a fluorescence microscopy technique with an intermediate-to-high optical resolution, but good optical sectioning capabilities and high speed. In contrast to epifluorescence microscopy only a thin slice of the sample is illuminated perpendicularly to the direction of observation. For illumination, a laser light-sheet is used, i.e. a laser beam which is focused only in one direction. A second method uses a circular beam scanned in one direction to create the lightsheet. As only the actually observed section is illuminated, this method reduces the photodamage and stress induced on a living sample. Also the good optical sectioning capability reduces the background signal and thus creates images with higher contrast, comparable to confocal microscopy. Because light sheet fluorescence microscopy scans samples by using a plane of light instead of a point, it can acquire images at speeds 100 to 1,000 times faster than those offered by point-scanning methods.
Vaa3D is an Open Source visualization and analysis software suite created mainly by Hanchuan Peng and his team at Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects. This software has been used in several large neuroscience initiatives and a number of applications in other domains. In a recent Nature Methods review article, it has been viewed as one of the leading open-source software suites in the related research fields. In addition, research using this software was awarded the 2012 Cozzarelli Prize from the National Academy of Sciences.
References
- ↑ Royer, Loïc A; Weigert, Martin; Günther, Ulrik; Maghelli, Nicola; Jug, Florian; Sbalzarini, Ivo F.; Myers, Eugene W. (2015). "ClearVolume – Open-source live 3D visualization for light sheet microscopy" . Nature Methods. 12 (6): 480–481. doi:10.1038/nmeth.3372. PMID 26020498. S2CID 205423715.