Orange is an open-source data visualization, machine learning and data mining toolkit. It features a visual programming front-end for exploratory qualitative data analysis and interactive data visualization. == Description == Orange is a component-based visual programming software package for data visualization, machine learning, data mining, and data analysis. Orange components are called widgets. They range from simple data visualization, subset selection, and preprocessing to empirical evaluation of learning algorithms and predictive modeling. Visual programming is implemented through an interface in which workflows are created by linking predefined or user-designed widgets, while advanced users can use Orange as a Python library for data manipulation and widget alteration. == Software == Orange is an open-source software package released under GPL and hosted on GitHub. Versions up to 3.0 include core components in C++ with wrappers in Python. From version 3.0 onwards, Orange uses common Python open-source libraries for scientific computing, such as numpy, scipy and scikit-learn, while its graphical user interface operates within the cross-platform Qt framework. The default installation includes a number of machine learning, preprocessing and data visualization algorithms in 6 widget sets (data, transform, visualize, model, evaluate and unsupervised). Additional functionalities are available as add-ons (text-mining, image analytics, bioinformatics, etc.). Orange is supported on macOS, Windows and Linux and can also be installed from the Python Package Index repository (pip install Orange3). == Features == Orange consists of a canvas interface onto which the user places widgets and creates a data analysis workflow. Widgets offer basic functionalities such as reading the data, showing a data table, selecting features, training predictors, comparing learning algorithms, visualizing data elements, etc. The user can interactively explore visualizations or feed the selected subset into other widgets. Canvas: graphical front-end for data analysis Widgets: Data: widgets for data input, data filtering, sampling, imputation, feature manipulation and feature selection Visualize: widgets for common visualization (box plot, histograms, scatter plot) and multivariate visualization (mosaic display, sieve diagram). Classify: a set of supervised machine learning algorithms for classification Regression: a set of supervised machine learning algorithms for regression Evaluate: cross-validation, sampling-based procedures, reliability estimation and scoring of prediction methods Unsupervised: unsupervised learning algorithms for clustering (k-means, hierarchical clustering) and data projection techniques (multidimensional scaling, principal component analysis, correspondence analysis). == Add-ons == Orange users can extend their core set of components with components in the add-ons. Supported add-ons include: Associate: components for mining frequent itemsets and association rule learning. Bioinformatics: components for gene expression analysis, enrichment, and access to expression databases (e.g., Gene Expression Omnibus) and pathway libraries. Data fusion: components for fusing different data sets, collective matrix factorization, and exploration of latent factors. Educational: components for teaching machine learning concepts, such as k-means clustering, polynomial regression, stochastic gradient descent, ... Explain: provides an extension with components for the model explanation, including Shapley value analysis Geo: components for working with geospatial data. Image analytics: components for working with images and ImageNet embeddings Network: components for graph and network analysis. Text mining: components for natural language processing and text mining. Time series: widget components for time series analysis and modeling. Single-cell: support for single-cell gene expression analysis, including components for loading single-cell data, filtering and batch effect removal, marker genes discovery, scoring of cells and genes, and cell type prediction. Spectroscopy: components for analyzing and visualization of (hyper)spectral datasets. Survival analysis: add-on for data analysis dealing with survival data. It includes widgets for standard survival analysis techniques, such as the Kaplan-Meier plot, the Cox regression model, and several derivative widgets. World Happiness: support for downloading socioeconomic data from a database, including OECD and World Development Indicators. Provides access to thousands of country indicators from various economic databases. Fairness: add-on for evaluation and creation of fair machine learning models without discrimination. Widgets range from computing fairness metrics like statistical parity to post-, pre-, in-processing methods to build fair models. == Objectives == The program provides a platform for experiment selection, recommendation systems, and predictive modelling and is used in biomedicine, bioinformatics, genomic research, and teaching. In science, it is used as a platform for testing new machine learning algorithms and for implementing new techniques in genetics and bioinformatics. In education, it was used for teaching machine learning and data mining methods to students of biology, biomedicine, and informatics. == Extensions == Various projects build on Orange either by extending the core components with add-ons or using only the Orange Canvas to exploit the implemented visual programming features and GUI. OASYS — ORange SYnchrotron Suite scOrange — single cell biostatistics Quasar — data analysis in natural sciences == History == In 1996, the University of Ljubljana and Jožef Stefan Institute started development of ML, a machine learning framework in C++, and Python bindings were developed for this framework in 1997, which, together with emerging Python modules, formed a joint framework called Orange. Over the following years, most contemporary major algorithms for data mining and machine learning were implemented in C++ (Orange's core) or Python modules. In 2002, first prototypes to create a flexible graphical user interface were designed using Pmw Python megawidgets. In 2003, the graphical user interface was redesigned and re-developed for Qt framework using PyQt Python bindings. The visual programming framework was defined, and the development of widgets (graphical components of the data analysis pipeline) began. In 2005, extensions for data analysis in bioinformatics was created. In 2008, Mac OS X DMG and Fink-based installation packages were developed. In 2009, over 100 widgets were created and maintained. In 2009, Orange 2.0 beta was released, offering installation packages on the website based on the daily compiling cycle. In 2012, a new object hierarchy was imposed, replacing the old module-based structure. In 2013, a significant redesign of the graphical user interface included a new toolbox and depiction of workflows. In 2015, Orange 3.0 was released. Orange stores the data in NumPy arrays; machine learning algorithms mostly use scikit-learn. In 2015, a text analysis add-on for Orange3 was released. In 2016, Orange released version 3.3. Development scheduled a monthly cycle for stable releases. In 2016, Orange began development and release of an Image Analytics add-on, with server-side deep neural networks for image embedding In 2017, a Spectroscopy add-on for the analysis of spectral data was introduced. In 2017, Geo, an add-on for dealing with geo-location data and visualisation of geo maps was introduced In 2018, Orange began development and release of an add-on for single-cell data analysis. In 2019, Orange separated its graphical interface for development as a separate project, orange-canvas-core In 2020, Orange introduced the Explain add-on with widgets for explaining classification models and regression models, highlighting the strength and contributions specific features make towards predicting a specific class. In 2022, World Happiness, an add-on for the Orange3 data mining suite, was introduced, providing widgets for accessing socioeconomic data from various databases such as World Happiness Report, World Development Indicators, OECD. In 2022, Orange extended the Explain add-on with an Individual Conditional Expectation plot and the Permutation Feature Importance technique. In 2023, Orange introduced the Fairness add-on, including widgets to calculate bias metrics, as well as widgets for pre-, post-, and in-processing methods, allowing the creation of models less susceptible to systematic error due to the vagaries of the data set.
Socially assistive robot
A socially assistive robot (SAR) aids users through social engagement and support rather than through physical tasks and interactions. == Background == The field of socially assistive robotics emerged in the early 2000s, following the emergence of the field of social robots. In contrast to social robots, SARs aid users with specific goals related to behavior change rather than serving as purely social entities. The term "Socially assistive robot" was initially defined by Maja Matarić and David Feil-Seifer in 2005. Since its inception, the field has gained substantial recognition, featuring numerous research projects, a wealth of global research publications, startup companies, and a growing array of products on the consumer market. The COVID-19 pandemic has underscored the immense potential of socially assistive robots, particularly in addressing the needs of large user populations, including children engaged in remote learning, elderly individuals grappling with loneliness, and those affected by social isolation and its associated negative consequences. == Characteristics of interaction == SARs rely on artificial intelligence (AI) to generate real-time, responsive, natural, and meaningful robot behaviors during interactions with humans. The robots employ various forms of communication, such as facial expressions, gestures, body movements, and speech. In contrast to robots intended for physical tasks, SARs are designed to support and motivate users to perform their own tasks. The tasks a user engages in can be physical (e.g., rehabilitation exercises for post-stroke users), cognitive (e.g., dementia screening for elderly users), or social (e.g., turn-taking for users with autism spectrum disorders). This complex interaction involves detecting and interpreting the user's movement, behavior, intent, goals, speech, and preferences. Machine learning and robot learning techniques are frequently employed to enhance the robot's understanding of the user, predict user preferences, and provide effective assistance. The effectiveness of socially assistive robots is assessed based on objective measurements of user performance and improvement resulting from the robot’s assistance and support. Unlike other branches of robotics, where effectiveness depends on the robot's physical task completion, SAR measures the success of the robot based on the user's progress and achievements. This evaluation is carried out using quantitative objective metrics, such as time spent on tasks, accuracy, retention, and verbalization, as well as quantitative subjective metrics, such as user survey tools. SAR is based on the large body of evidence showing that users tend to respond more positively to interactions with physical robots compared to interactions with screens. Interaction with physical robots also encourages users to learn and retain more information than screen-based interactions. This fundamental insight underlines why physical robots in SAR applications are more effective, as opposed to interactions solely involving screens, tablets, or computers. == Uses and applications == SARs have been developed and validated in a wide array of applications, including healthcare, elder care, education, and training. For example, SARs have been developed to support children on the autism spectrum in acquiring and practicing social and cognitive skills, to motivate and coach stroke patients throughout their rehabilitation exercises, monitoring individuals health (ex. fall detection), and to encourage elderly users to be more physically and socially active. There is a concern that technophobia and lack of trust in robots will pose a barrier to the effectiveness of SARs in older adults.
Smart environment
Smart environments link computers and other smart devices to everyday settings and tasks. Smart environments include smart homes, smart cities, and smart manufacturing. == Introduction == Smart environments are an extension of pervasive computing. According to Mark Weiser, pervasive computing promotes the idea of a world that is connected to sensors and computers. These sensors and computers are integrated with everyday objects in peoples' lives and are connected through networks. == Definition == Cook and Das, define a smart environment as "a small world where different kinds of smart devices are continuously working to make inhabitants' lives more comfortable." Smart environments aim to satisfy the experience of individuals from every environment, by replacing hazardous work, physical labor, and repetitive tasks with automated agents. Poslad differentiates three different kinds of smart environments for systems, services, and devices: virtual (or distributed) computing environments, physical environments, and human environments, or a hybrid combination of these: Virtual computing environments enable smart devices to access pertinent services anywhere and anytime. Physical environments may be embedded with various smart devices of different types including tags, sensors, and controllers, and have different form factors ranging from nano- to micro- to macro-sized. Human environments: humans, either individually or collectively, inherently form a smart environment for devices. However, humans themselves may be accompanied by smart devices such as mobile phones, use surface-mounted devices (wearable computing), and contain embedded devices (e.g., pacemakers to maintain a healthy heart operation or AR contact lenses) == Features == Smart environments encompass a range of features and services across various domains, including smart homes, smart cities, smart health, and smart factories. Some of the key features of smart environments are: Sensors and Actuators: Smart environments are equipped with an assembly of sensors and actuators that collect data and initiate actions to provide services for the betterment of human life. Interconnected Systems: These environments consist of interconnected systems that enable seamless communication and coordination among various devices and components. Data-Driven Technologies: Smart environments leverage data-driven technologies, such as the Internet of Things (IoT), to obtain information from the physical world, process it, and perform actions accordingly. Efficiency and Sustainability: They are designed to improve efficiency, sustainable practices, and resource management across different settings, such as energy efficiency in smart homes and environmental quality management in smart cities. Diverse Requirements: Different types of smart environments have diverse requirements and technology choices, influencing the processing and utilization of data within a specific environment. == Technologies == Building a smart environment involves technologies of Wireless communication Algorithm design, signal prediction & classification, information theory Multilayered software architecture, Corba, middleware Speech recognition Image processing, image recognition Sensors design, calibration, motion detection, temperature, pressure sensors, accelerometers Semantic Web and knowledge graphs Adaptive control, Kalman filters Computer networking Parallel processing Operating systems == Existing projects == The Aware Home Research Initiative at Georgia Tech "is devoted to the multidisciplinary exploration of emerging technologies and services based in the home" and was launched in 1998 as one of the first "living laboratories." The Mav Home (Managing an Adaptive Versatile Home) project, at UT Arlington, is a smart environment-lab with state-of-the-art algorithms and protocols used to provide a customized, personal environment to the users of this space. The Mav Home project, in addition to providing a safe environment, wants to reduce the energy consumption of the inhabitants. Other projects include House at the MIT Media Lab and many others.
Masking (art)
In art, craft, and engineering, masking is the use of materials to protect areas from change, or to focus change on other areas. This can describe either the techniques and materials used to control the development of a work of art by protecting a desired area from change; or a phenomenon that (either intentionally or unintentionally) causes a sensation to be concealed from conscious attention. The term is derived from the word mask, in the sense that it hides the face from view. == In painting == Masking materials supplement a painter's dexterity and choice of applicator to control where paint is laid. Examples include the use of a stencil or masking tape to protect areas which are not to be painted. === Solid masks === Most solid masks require an adhesive to hold the mask in place while work is performed. Some, such as masking tape and frisket, come with adhesive pre-applied. Solid masks are readily available in bulk, and are used in large painting jobs. Paper products Kraft paper Butcher paper Masking tape Plastic film Frisket Polyester tape Stencils Silk screen === Liquid masks === Liquid masks are preferred where precision is needed; they prevent paint from seeping underneath, resulting in clean edges. Care must be taken to remove them without damaging the work underneath. Latex or other polymers Molten wax Gesso, typically a substrate for painting, but can also be applied to achieve masking effects == In photography == Masks used for photography are used to enhance the quality of an image. Representations of a scene—whether film, video display, or printed—do not have the dynamic contrast range available to the human eye looking directly at the same scene. Adjusting the contrast in an image helps restore some of the perceived qualities of the original scene. These adjustments are typically performed on "blown-out" highlights, and "crushed" or "muddy" shadow areas, where clipping has occurred; or on desaturated colors. Photographic masks are peculiar in that they are produced from the image they will alter, an exercise in recursion. Masks used to produce other effects are similar to those used in painting. === Controlling exposure === ==== Film ==== The basic methods of controlling exposure are dodging and burning, which respectively lighten (reduce exposure) and darken (increase exposure) areas of an image. The tools a film photographer uses range from shaped pieces of black material (such as studio foil, foam, and paper) to the photographer's hands. To create a photographic mask, a sheet of negative film is contact-exposed to the original film negative or slide positive in a particular way. Both films are then combined to produce a processed positive. The process is similar when applied using digital techniques: the inverse of the working image is reduced to an image mask; filters or other adjustments are then applied, using the mask to selectively block portions of the image. ==== Digital ==== Image editors offer at the very least a "Select All" command and a rectangular "marquee" selection tool. (The word "marquee" describes the "crawling ants" border used to highlight the active region.) Once a selection is created, further changes to the image will be confined to that area. To continue editing the rest of the image, the selection is either "deselected" or the entire image is selected. Advanced suites offer more ways to select portions of an image, as well as ways to combine these selections through. Selection masks can be switched between an editable greyscale image and a mask. They allow the user to create a mask using the suite's painting tools. === Contrast masking === When the contrast range of an image needs to be adjusted, a contrast mask is a simple solution. The processed image resembles what would be achieved when exposing through a neutral density filter, but the effects are focused highly upon the extreme regions of the image. The blocking areas of the mask coincide with the highlights of the image, and the permissive areas with the shadows, resulting in more detail appearing in each. ==== Film ==== The mask is often made from high-quality black-and-white film, such as Kodak Technical Pan, which allows for a degree of softening on the mask. Its processing time is reduced so as to not completely oppose the original negative. Both negatives are combined and registered, and collectively exposed with additional time to compensate for the presence of the mask. ==== Digital ==== Contrast masking is made simpler with digital editing. A grayscale version of the image is produced, either by desaturation or by calculating selected ratios of the image's color channels, inverted, and blurred. The mask and original image are blended together to produce the final processed image. Some image editors allow for refinement of the effect by changing the strength of the blend. Contrast masking can be considered to be the opposite of gamma correction, which adjusts the midtones of an image. Effects similar to contrast masking can be achieved by adjusting the response curves of an image. === Unsharp masking === A derivative of contrast masking is unsharp masking, an unusual term for a process intended to increase the apparent sharpness (acutance) of an image. Unsharp masking uses a blurred form of the image to increase contrast along regions of moderate contrast difference. Around edges, the blur region causes highlights to overexpose and shadows to underexpose. Taken to an extreme, the edges become overly visible and detract from the quality of the image—this is referred to as halation. Unsharp masking does not increase the actual sharpness, as it cannot recover details lost to blurring. ==== Film ==== Unsharp masking allows the photographer to sharpen areas that have become blurred in the original negative, due to long shutter speed/exposure time, or from using a wide aperture/"fast" lens. When creating the unsharp mask, extra space or diffusing material is added between the image and the mask to produce the necessary blur. ==== Digital ==== Unsharp masking has become automated in digital editing, with higher-end suites offering the process as a "tool" or "filter" in their standard sharpening kits—the actual creation of a mask is bypassed in favor of calculations that represent the mask's effect. The process depends on three factors: the radius of the blur, the strength of the effect, and the threshold degree of contrast above which the effect will be applied. (Adjusting the threshold allows the editor to apply the effect selectively upon moderately defined edges and ignore image noise.) Unsharp masking is computationally more complex than other sharpening algorithms, but results in a higher-quality remedy. Deconvolution allows for truer sharpening, but is much more complex than unsharp masking.
Bump (application)
Bump was an iOS and Android mobile app that enabled smartphone users to transfer contact information, photos and files between devices. In 2011, it was #8 on Apple's list of all-time most popular free iPhone apps, and by February 2013 it had been downloaded 125 million times. Its developer, Bump Technologies, shut down the service and discontinued the app on January 31, 2014, after being acquired by Google for Google Photos and Android Camera. == Features == Bump sent contact information, photos and files to another device over the internet. Before activating the transfer, each user confirmed what they want to send to the other user. To initiate a transfer, two people physically bumped their phones together. A screen appeared on both users' smartphone displays, allowing them to confirm what they want to send to each other. When two users bumped their phones, software on the phones send a variety of sensor data to an algorithm running on Bump servers, which included the location of the phone, accelerometer readings, IP address, and other sensor readings. The algorithm figured out which two phones felt the same physical bump and then transfers the information between those phones. Bump did not use Near Field Communication. February 2012 release of Bump 3.0 for iOS, the company streamlined the app to focus on its most frequently used features: contact and photo sharing. Bump 3.0 for Android maintained the features eliminated from the iOS version but moved them behind swipeable layers. In May 2012, a Bump update enabled users to transfer photos from their phone to their computer via a web service. To initiate a transfer, the user goes to the Bump website on their computer and bumps the smartphone on the computer keyboard's space bar. By December 2012, various Bump updates for iOS and Android had added the abilities to share video, audio, and any files. Users swipe to access those features. In February 2013, an update to the Bump iOS and Android apps enabled users to transfer photos, videos, contacts and other files from a computer to a smartphone and vice versa via a web service. To perform the transfer, users went to the Bump website on their computer and bump the smartphone on the computer keyboard's space bar. == History == The underlying idea of a synchronous gesture like bumping two devices for content transfer or pairing them was first conceived by Ken Hinkley of Microsoft Research in 2003. This idea was presented at a user interface and technology conference that same year. The paper proposed the use of accelerometers and a bumping gesture of two devices to enable communication, screen sharing and content transfer between them. Similar to this original concept, the idea for Bump app was conceived by David Lieb, a former employee of Texas Instruments, while he was attending the University of Chicago Booth School of Business for his MBA. While going through the orientation and meeting process of business school, he became frustrated by constantly entering contact information into his iPhone and felt that the process could be improved. His fellow Texas Instruments employees Andy Huibers and Jake Mintz, who was a classmate of Lieb's at the University of Chicago's MBA program, joined Lieb to form Bump Technologies. Bump Technologies launched in 2008 and is located in Mountain View, CA. Early funding for the project was provided by startup incubator Y Combinator, Sequoia Capital and other angel investors. It gained attention at the CTIA international wireless conference, due to its accessibility and novelty factor. In October 2009, Bump received $3.4m in Series A funding followed in January 2011 with a $16m series B financing round led by Andreessen Horowitz. Silicon Valley venture capitalist Marc Andreessen sits on the company's board. The Bump app debuted in the Apple iOS App Store in March 2009 and was “one of the apps that helped to define the iPhone” (Harry McCracken, Technologizer). It soon became the billionth download on Apple's App Store. An Android version launched in November 2009. By the time Bump 3.0 for iOS was released in February 2012, the app had been installed 77 million times, with users sharing more than 2 million photos daily. As of February 2013, there had been 125 million Bump app downloads. == Other apps created by Bump Technologies == Bump Technologies worked with PayPal in March 2010 to create a PayPal iPhone application. The application, which allows two users to automatically activate an Internet transfer of money between their accounts, found widespread adoption. A similar version was released for Android in August 2010. The Bump capability in PayPal's apps was removed in March 2012. At that time, Bump Technologies released Bump Pay, an iOS app that lets users transfer money via PayPal by physically bumping two smartphones together. The tool was originally created for the Bump team to use when splitting up restaurant bills. The payment feature was not added to the Bump app because the company “wanted to make it as simple as possible so people understand how this works,” Lieb told ABC News. Bump Pay was the first app from the company's Bump Labs initiative. A goal of Bump Labs is to test new app ideas that may not fit within the main Bump app. ING Direct added a feature to its iPhone app in 2011 that lets users transfer money to each other using Bump's technology. The feature was later added to its Android app, now called Capital One 360. In July 2012, Bump Technologies released Flock, an iPhone photo sharing app. An Android version was released in December 2012. Using geolocation data embedded in photos and a user's Facebook connections, Flock finds pictures the user takes while out with friends and family and puts everyone's photos from that event into a single shared album. Users receive a push notification after the event, asking if they want to share their photos with friends who were there in the moment. The app will also scan previous photos in the iPhone camera roll and uncover photos that have yet to be shared. If location services were enabled at the time a photo was taken, Flock allows users to create an album of photos from the past with the friends who were there with them. == Acquisition by Google == On September 16, 2013, Bump Technologies announced that it had been acquired by Google. On December 31, 2013, they broke the news that both Bump and Flock would be discontinued so that the team could focus on new projects at Google. The apps were removed from the App Store and Google Play on January 31, 2014. The company subsequently deleted all user data and shut down their servers, thus rendering existing installations of the apps inoperable.
Biohybrid system
Biohybrid systems refer to the integration of biological materials, such as cells or tissues, with artificial components, including electronics or mechanical structure. This combination incorporates the capabilities of living organisms with the precision of man-made technology. As a result, these systems perform tasks that neither biology nor machines could achieve independently. Biohybrid systems might use lab-cultured muscle cells to power small robots or combine sensors with living tissue for better health sensing. The intent behind these systems is to combine the benefits of biological and technological components to introduce new solutions for complex medical challenges. Biohybrid systems may have transformative potential across sectors, such as robotics to create actuators and sensors that mimic natural muscle and nerve function, medicine in developing smart implants and drug delivery systems, in prosthetics for enhancing user control through neural or muscular interfaces and environmental sustainability for deploying biohybrid solutions for pollution sensing or remediation. == Origin == The term "biohybrid" is a compound of "bio" from biology (meaning life) and "hybrid" (referring to a combination of distinct elements), denoting a field of study. Its use helps distinguish such systems from purely biological constructs or entirely synthetic machines. Early academic mentions may include bio actuated robotics papers and foundational tissue-robot integration studies published in journals like Nature Biotechnology or Science Robotics. The emergence of the term reflects a growing recognition of the need to describe systems that do not fit cleanly into traditional categories. == Design principles == One of the most significant biohybrid challenges is to engineer interfaces between living tissue and artificial materials that are efficient. This means having precise control over adhesion at the surface, diffusion of nutrients, and signal conduction. Actuation mechanisms within the heart of these systems generate movement or mechanical response. These may be in the form of living muscle cells such as skeletal myocytes or cardiomyocytes, soft pneumatic actuators, or electrical stimulation-responsive tissues. Materials selection is equally critical. Hydrogels, elastomers like PDMS (polydimethylsiloxane), and biopolymers are commonly used due to their softness and biocompatibility. These materials must support cell viability, resist immune attack, and allow the integration of mechanical or electrical components. == Key components == At their core, biohybrid systems work by bridging living biological parts with technology. Through this integration, functionality that neither system could accomplish singularly is possible. Biological parts may be cells, tissues, or even organs—occasionally cultured in a laboratory setting. These biological parts carry out biologically inspired behaviors, such as muscle contraction or chemical sensing in the body. Technological components may constitute devices like sensors, electronic components, and mechanical structure. These manipulate the system, supply power, or transfer data. An example is a sensor that is implantable within a body and detects glucose levels as it sends information to a smart phone. By integrating these artificial and biological parts, biohybrid systems can perform advanced functions, such as tissue regeneration, real-time health monitoring, or the recovery of motor function in paralysis patients. Biohybrid systems generally consist of two major components: the biological and the mechanical. Biological components may include muscle cells for contraction, endothelial cells for vascularization, and stem cells for regenerative capabilities. Mechanical components comprise soft actuators that mimic organic motion, synthetic scaffolds that provide support and structure, and microfluidic systems that facilitate the delivery of nutrients and removal of waste. These components are combined in a manner that allows for dynamic, lifelike behavior—such as the contraction of tissue or the propagation of mechanical waves—while maintaining biocompatibility and durability. == Applications == The range of applications for biohybrid systems is broad and continuously expanding. In robotics, biohybrid structures have been used to engineer microscopic, muscle-driven machines, such as Harvard University's biohybrid stingray robot. In medical applications, they offer new alternatives for organ repair and augmentation, including biohybrid heart valves and esophageal scaffolds. Biohybrids are also promising in neural interfaces, where the goal is to create long-lasting, stable interaction between mechanical devices and brain tissue. Muscle-actuated drug response platforms are under exploration in pharmacology for modelling and real-time screening. == Examples == Several high-profile research projects have demonstrated the potential of biohybrid systems: Harvard researchers developed a biohybrid swimming ray powered by rat cardiac cells layered onto a gold skeleton, mimicking the motion of a real stingray. At the Massachusetts Institute of Technology, a cardiac pump actuated entirely by living heart muscle cells was engineered to simulate the behavior of a beating heart. Bio actuated soft robots have been built to simulate gut peristalsis, using muscle contractions to replicate natural wave-like movement in the digestive tract. == Challenges and limitations == As with many technologies that involve living systems, biohybrid systems raise important ethical and biomedical questions. Cell sourcing remains a key issue, particularly when embryonic or animal-derived cells are used. Long-term viability is another concern—living tissues must be kept alive with nutrients and oxygen, and they often degrade or elicit immune responses when implanted. Powering these biological parts presents logistical and ethical hurdles as well. Systems must either include internal mechanisms for nutrient delivery or be supported externally, which can limit portability and independence. == Future directions == Researchers are exploring self-directed, self-regulated organ substitutes and regenerative implants that can respond to their surroundings in real-time. These systems may be integrated with artificial intelligence to make them adjust to stimuli and coordinate complex behaviors. Future potential applications are wearable biohybrid systems for rehabilitation, space medicine devices for long-duration missions, and implantable devices that integrate into human physiology.
Amira (software)
Amira (ah-MEER-ah) 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. == Overview == Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. It is used by researchers and engineers in academia and industry. It is a tool for processing, analysis and visualization of data from various modalities; e.g. micro-CT, PET, Ultrasound. It is used in many fields, such as microscopy in biology and materials science, molecular biology, quantum physics, astrophysics, computational fluid dynamics (CFD), finite element modeling (FEM), non-destructive testing (NDT), and many more. One of the key features, besides data visualization, is Amira's set of tools for image segmentation and geometry reconstruction. This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis, density analysis, shape analysis, or the generation of 3D computer models for visualization, numerical simulations, or rapid prototyping or 3D printing. Other key Amira features are multi-planar and volume visualization, image registration, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data, skeletonization, spatial graph analysis, and stereoscopic rendering of 3D data over multiple displays and immersive virtual reality environments, including CAVEs. As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge. == History == === 1993–1998: Research software === Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department's mission is to help solve computationally and scientifically challenging tasks in medicine, biology, engineering and materials science. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products' interactivity, flexibility, and ease-of-use for non-computer scientists. Therefore, the development of a new software system was started in a research project within a medically oriented, multi-disciplinary collaborative research center. Based on experiences that Tobias Höllerer had gained in late 1993 with the new graphics library IRIS Inventor, it was decided to utilize that library. The development of the medical planning system was performed by Detlev Stalling, who later became the chief software architect of Amira. The new software was called "HyperPlan", highlighting its initial target application – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. The software was based on libraries such as OpenGL (originally IRIS GL), Open Inventor (originally IRIS Inventor), and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit. The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in medical image computing, medical visualization, neurobiology, confocal microscopy, flow visualization, molecular analytics and computational astrophysics. === 1998–today: Commercially supported product === The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB's primary mission was algorithmic research. Therefore, the spin-off company Indeed – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff. In Feb 1998 the HyperPlan software was given the new, application-neutral name "Amira". This name is not an acronym, but was chosen for being pronounceable in different languages and providing a suitable connotation, namely "to look at" or "to wonder at", from the Latin verb "admirare" (to admire), which reflects a basic situation in data visualization. A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths. Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years. In 2003 both Indeed – Visual Concepts GmbH, as well as TGS, Inc. were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury's newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences. In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. This brought the two software sisters Amira and Avizo back into one hand. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. In 2016 FEI has been bought by Thermo Fisher Scientific and became part of its Materials & Structural Analysis division in early 2017. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. In the meantime, the number of scientific articles using the Amira / Avizo software, is in the order of 10 thousands. == Amira options == === Microscopy option === Specific readers for microscopy data Image deconvolution Exploration of 3D imagery obtained from virtually any microscope Extraction and editing of filament networks from microscopy images === DICOM reader === Import of clinical and preclinical data in DICOM format === Mesh option === Generation of 3D finite element (FE) meshes from segmented image data Support for many state-of-the-art FE solver formats High-quality visualization of simulation mesh-based results, using scalar, vector, and tensor field display modules === Skeletonization option === Reconstruction and analysis of neural and vascular networks Visualization of skeletonized networks Length and diameter quantification of network segments Ordering of segments in a tree graph Skeletonization of very large image stacks === Molecular option === Advanced tools for the visualization of molecule models Hardware-accelerated volume rendering Powerful molecule editor Specific tools for complex molecular visualization === Developer option === Creation of new custom components for visualizing or data processing Implementation of new file readers or writers C++ programming language Development wizard for getting started quickly === Neuro option === Medical image analysis for DTI and brain perfusion Fiber tracking supporting several stream-line based algorithms Fiber separation into fiber bundles based on user defined source and destination regions Computation of tensor fields, diffusion weighted maps Eigenvalue decomposition of tensor fields Computation of mean transit time, cerebral blood flow, and cerebral blood volume === VR option === Visualization of data on large tiled displays