Elastix (image registration)

Elastix (image registration)

Elastix is an image registration toolbox built upon the Insight Segmentation and Registration Toolkit (ITK). It is entirely open-source and provides a wide range of algorithms employed in image registration problems. Its components are designed to be modular to ease a fast and reliable creation of various registration pipelines tailored for case-specific applications. It was first developed by Stefan Klein and Marius Staring under the supervision of Josien P.W. Pluim at Image Sciences Institute (ISI). Its first version was command-line based, allowing the final user to employ scripts to automatically process big data-sets and deploy multiple registration pipelines with few lines of code. Nowadays, to further widen its audience, a version called SimpleElastix is also available, developed by Kasper Marstal, which allows the integration of elastix with high level languages, such as Python, Java, and R. == Image registration fundamentals == Image registration is a well-known technique in digital image processing that searches for the geometric transformation that, applied to a moving image, obtains a one-to-one map with a target image. Generally, the images acquired from different sensors (multimodal), time instants (multitemporal), and points of view (multiview) should be correctly aligned to proceed with further processing and feature extraction. Even though there are a plethora of different approaches to image registration, the majority is composed of the same macro building blocks, namely the transformation, the interpolator, the metric, and the optimizer. Registering two or more images can be framed as an optimization problem that requires multiple iterations to converge to the best solution. Starting from an initial transformation computed from the image moments the optimization process searches for the best transformation parameters based on the value of the selected similarity metric. The figure on the right shows the high-level representation of the registration of two images, where the reference remains constant during the entire process, while the moving one will be transformed according to the transformation parameters. In other words, the registration ends when the similarity metric, which is a mathematical function with a certain number of parameters to be optimized, reaches the optimal value which is highly dependent on the specific application. == Main building blocks == Following the structure of the image registration workflow, the elastix toolbox proposes a modular solution that implements for each of the building blocks different algorithms, highly employed in medical image registration, and helps the final users to build their specific pipeline by selecting the most suitable algorithm for each of the main building blocks. Each block is easily configurable both by selecting pre-defined initialization values or by trying multiple sets of parameters and then choosing the most performing one. The registration is performed on images, and the elastix toolbox supports all the data formats supported by ITK, ranging from JPEG and PNG to medical standard formats such as DICOM and NIFTI. It also stores physical pixel spacing, the origin and the relative position to an external world reference system, when provided in the metadata, to facilitate the registration process, especially in medical field applications. === Transformation === The transformation is an essential building block, since it defines the allowable transformations. In image registration, the main distinction can be done between parallel-to-parallel and parallel-to-non parallel (deformable) line mapping transformations. In the elastix toolbox, the final users can select one transformation or compose more transformations either through addition or via composition. Below are reported the different transformation models in order of increasing flexibility, along with the corresponding elastix class names between brackets. Translation (TranslationTransform) allows only translations Rigid (EulerTransform) expands the translation adding rotations and the object is seen as a rigid body Similarity (SimilarityTransform) expands the rigid transformation by introducing isotropic scaling Affine (AffineTransform) expands the rigid transformation allowing both scaling and shear B-splines (BSplineTransform) is a deformable transformation usually preceded by a rigid or affine one Thin-plate splines (SplineKernelTransform) is a deformable transformation belonging to the class of kernel-based transformations that is a composition of and affine and a non-rigid part === Metric === The similarity metric is the mathematical function whose parameters should be optimized to reach the desired registration, and, during the process, it is computed multiple times. Below are reported the available metrics computed employing the reference and the transformed images and the corresponding elastix class names between brackets. Mean squared difference (AdvancedMeanSquares) to be used for mono-modal applications Normalized correlation coefficient (AdvancedNormalizedCorrelation) to be used for images that have an intensity linear relationship Mutual information (AdvancedMattesMutualInformation) to be used for both mono- and multi-modal applications and optimized to reach better performance compared to the normalized version Normalized mutual information (NormalizedMutualInformation) for both mono- and multi-modal applications Kappa statistic (AdvancedKappaStatistic) to be used only for binary images === Sampler === For the computation of the similarity metrics, it is not always necessary to consider all the voxels and, sometimes, it can be useful to use only a fraction of the voxels of the images, i.e. to reduce the execution time for big input images. Below are reported the available criteria for selecting a fraction of the voxels for the similarity metric computation and the corresponding elastix class names between brackets. Full (Full) to employ all the voxels Grid (Grid) to employ a regular grid defined by the user to downsample the image Random (Random) to randomly select a percentage of voxels defined by the users (all voxels have equal probability to be selected) Random coordinate (RandomCoordinate) like the random criterion, but in this case also off-grid positions can be selected to simplify the optimization process === Interpolator === After the application of the transformation, it may occur that the voxels used for the similarity metric computation are at non-voxel positions, so intensity interpolation should be performed to ensure the correctness of the computed values. Below are reported the implemented interpolators and the corresponding elastix class names between brackets. Nearest neighbor (NearestNeighborInterpolator) exploits little resources, but gives low quality results Linear (LinearInterpolator) is sufficient in general applications N-th order B-spline (BSplineInterpolator) can be used to increase the order N, increasing quality and computation time. N=0 and N=1 indicate the nearest neighbor and linear cases respectively. === Optimizer === The optimizer defines the strategy employed for searching the best transformation parameter to reach the correct registration, and it is commonly an iterative strategy. Below are reported some of the implemented optimization strategies. Gradient descent Robbins-Monro, similar to the gradient descent, but employing an approximation of the cost function derivatives A wider range of optimizers is also available, such as Quasi-Newton or evolutionary strategies. === Other features === The elastix software also offers other features that can be employed to speed up the registration procedure and to provide more advanced algorithms to the end-users. Some examples are the introduction of blur and Gaussian pyramid to reduce data complexity, and multi-image and multi-metric framework to deal with more complex applications. == Applications == Elastix has applications mainly in the medical field, where image registration is fundamental to get comprehensive information regarding the analysed anatomical region. It is widely employed in image-guided surgery, tumour monitoring, and treatment assessment. For example, in radiotherapy planning, image registration allows to correctly deliver the treatment and evaluate the obtained results. Thanks to the wide range of implemented algorithms, the use of the elastix software allows physicians and researchers to test different registration pipelines from the simplest to more complex ones, and to save the best one as a configuration file. This file and the fact that the software is completely open-source makes it easy to reproduce the work, that can help supporting the open science paradigm, and allows fast reuse on different patients data. In image-guided surgery, registration time and accuracy are critical points, considering that, during the registration, the patient is on the operating table, and the imag

Networked Help Desk

Networked Help Desk is an open standard initiative to provide a common API for sharing customer support tickets between separate instances of issue tracking, bug tracking, customer relationship management (CRM) and project management systems to improve customer service and reduce vendor lock-in. The initiative was created by Zendesk in June 2011 in collaboration with eight other founding member organizations including Atlassian, New Relic, OTRS, Pivotal Tracker, ServiceNow and SugarCRM. The first integration, between Zendesk and Atlassian's issue tracking product, Jira, was announced at the 2011 Atlassian Summit. By August 2011, 34 member companies had joined the initiative. A year after launching, over 50 organizations had joined. Within Zendesk instances this feature is branded as ticket sharing. == Basis == Support tools are generally built around a common paradigm that begins with a customer making a request or an incident report, these create a ticket. Each ticket has a progress status and is updated with annotations and attachments. These annotations and attachments may be visible to the customer (public), or only visible to analysts (private). Customers are notified of progress made on their ticket until it is complete. If the people necessary to complete a ticket are using separate support tools, additional overhead is introduced in maintaining the relevant information in the ticket in each tool while notifying the customer of progress made by each group in completing their ticket. For example, if a customer support issue is caused by a software bug and reported to a help desk using one system, and then the fix is documented by the developers in another, and analyzed in a customer relationship management tool, keeping the records in each system up-to-date and notifying the customer manually using a swivel chair approach is unnecessarily time-consuming and error-prone. If information is not transferred correctly, a customer may have to re-explain their problem each time their ticket is transferred. For systems with the Networked Help Desk API implemented, it is possible for several different applications related to a customer's support experience to synchronize data in one uniquely identified shared ticket. While many applications in these domains have implemented APIs that allow data to be imported, exported and modified, Network Help Desk provide a common standard for customer support information to automatically synchronize between several systems. Once implemented, two systems can quickly share tickets with just a configuration change as they both understand the same interface. Communication between two instances on a specific ticket occurs in three steps, an invitation agreement, sharing of ticket data and continued synchronization of tickets. The standard allows for "full delegation" (analysts in both systems each make public and private comments and synchronize status) as well as "partial delegation" where the instance receiving the ticket can only make private comments and status changes are not synchronized. Tickets may be shared with multiple instances. == Implementation list ==

Situated approach (artificial intelligence)

In artificial intelligence research, the situated approach builds agents that are designed to behave effectively successfully in their environment. This requires designing AI "from the bottom-up" by focussing on the basic perceptual and motor skills required to survive. The situated approach gives a much lower priority to abstract reasoning or problem-solving skills. The approach was originally proposed as an alternative to traditional approaches (that is, approaches popular before 1985 or so). After several decades, classical AI technologies started to face intractable issues (e.g. combinatorial explosion) when confronted with real-world modeling problems. All approaches to address these issues focus on modeling intelligences situated in an environment. They have become known as the situated approach to AI. == Emergence of a concept == === From traditional AI to Nouvelle AI === During the late 1980s, the approach now known as Nouvelle AI (Nouvelle means new in French) was pioneered at the MIT Artificial Intelligence Laboratory by Rodney Brooks. As opposed to classical or traditional artificial intelligence, Nouvelle AI purposely avoided the traditional goal of modeling human-level performance, but rather tries to create systems with intelligence at the level of insects, closer to real-world robots. But eventually, at least at MIT new AI did lead to an attempt for humanoid AI in the Cog Project. === From Nouvelle AI to behavior-based and situated AI === The conceptual shift introduced by nouvelle AI flourished in the robotics area, given way to behavior-based robotics (BBR), a methodology for developing AI based on a modular decomposition of intelligence. It was made famous by Rodney Brooks: his subsumption architecture was one of the earliest attempts to describe a mechanism for developing BBAI. It is extremely popular in robotics and to a lesser extent to implement intelligent virtual agents because it allows the successful creation of real-time dynamic systems that can run in complex environments. For example, it underlies the intelligence of the Sony Aibo and many RoboCup robot teams. Realizing that in fact all these approaches were aiming at building not an abstract intelligence, but rather an intelligence situated in a given environment, they have come to be known as the situated approach. In fact, this approach stems out from early insights of Alan Turing, describing the need to build machines equipped with sense organs to learn directly from the real-world instead of focusing on abstract activities, such as playing chess. == Definitions == Classically, a software entity is defined as a simulated element, able to act on itself and on its environment, and which has an internal representation of itself and of the outside world. An entity can communicate with other entities, and its behavior is the consequence of its perceptions, its representations, and its interactions with the other entities. === AI loop === Simulating entities in a virtual environment requires simulating the entire process that goes from a perception of the environment, or more generally from a stimulus, to an action on the environment. This process is called the AI loop and technology used to simulate it can be subdivided in two categories. Sensorimotor or low-level AI deals with either the perception problem (what is perceived?) or the animation problem (how are actions executed?). Decisional or high-level AI deals with the action selection problem (what is the most appropriate action in response to a given perception, i.e. what is the most appropriate behavior?). === Traditional or symbolic AI === There are two main approaches in decisional AI. The vast majority of the technologies available on the market, such as planning algorithms, finite-state machines (FSA), or expert systems, are based on the traditional or symbolic AI approach. Its main characteristics are: It is top-down: it subdivides, in a recursive manner, a given problem into a series of sub-problems that are supposedly easier to solve. It is knowledge-based: it relies on a symbolic description of the world, such as a set of rules. However, the limits of traditional AI, which goal is to build systems that mimic human intelligence, are well-known: inevitably, a combinatorial explosion of the number of rules occurs due to the complexity of the environment. In fact, it is impossible to predict all the situations that will be encountered by an autonomous entity. === Situated or behavioral AI === In order to address these issues, another approach to decisional AI, also known as situated or behavioral AI, has been proposed. It does not attempt to model systems that produce deductive reasoning processes, but rather systems that behave realistically in their environment. The main characteristics of this approach are the following: It is bottom-up: it relies on elementary behaviors, which can be combined to implement more complex behaviors. It is behavior-based: it does not rely on a symbolic description of the environment, but rather on a model of the interactions of the entities with their environment. The goal of situated AI is to model entities that are autonomous in their environment. This is achieved thanks to both the intrinsic robustness of the control architecture, and its adaptation capabilities to unforeseen situations. === Situated agents === In artificial intelligence and cognitive science, the term situated refers to an agent which is embedded in an environment. The term situated is commonly used to refer to robots, but some researchers argue that software agents can also be situated if: they exist in a dynamic (rapidly changing) environment, which they can manipulate or change through their actions, and which they can sense or perceive. Examples might include web-based agents, which can alter data or trigger processes (such as purchases) over the Internet, or virtual-reality bots which inhabit and change virtual worlds, such as Second Life. Being situated is generally considered to be part of being embodied, but it is useful to consider each perspective individually. The situated perspective emphasizes that intelligent behavior derives from the environment and the agent's interactions with it. The nature of these interactions are defined by an agent's embodiment. == Implementation principles == === Modular decomposition === The most important attribute of a system driven by situated AI is that the intelligence is controlled by a set of independent semi-autonomous modules. In the original systems, each module was actually a separate device or was at least conceived of as running on its own processing thread. Generally, though, the modules are just abstractions. In this respect, situated AI may be seen as a software engineering approach to AI, perhaps akin to object oriented design. Situated AI is often associated with reactive planning, but the two are not synonymous. Brooks advocated an extreme version of cognitive minimalism which required initially that the behavior modules were finite-state machines and thus contained no conventional memory or learning. This is associated with reactive AI because reactive AI requires reacting to the current state of the world, not to an agent's memory or preconception of that world. However, learning is obviously key to realistic strong AI, so this constraint has been relaxed, though not entirely abandoned. === Action selection mechanism === The situated AI community has presented several solutions to modeling decision-making processes, also known as action selection mechanisms. The first attempt to solve this problem goes back to subsumption architectures, which were in fact more an implementation technique than an algorithm. However, this attempt paved the way to several others, in particular the free-flow hierarchies and activation networks. A comparison of the structure and performances of these two mechanisms demonstrated the advantage of using free-flow hierarchies in solving the action selection problem. However, motor schemas and process description languages are two other approaches that have been used with success for autonomous robots. == Notes and references == Arsenio, Artur M. (2004) Towards an embodied and situated AI, In: Proceedings of the International FLAIRS conference, 2004. (online) The Artificial Life Route To Artificial Intelligence: Building Embodied, Situated Agents, Luc Steels and Rodney Brooks Eds., Lawrence Erlbaum Publishing, 1995. (ISBN 978-0805815184) Rodney A. Brooks Cambrian Intelligence (MIT Press, 1999) ISBN 0-262-52263-2; collection of early papers including "Intelligence without representation" and "Intelligence without reason", from 1986 & 1991 respectively. Ronald C. Arkin Behavior-Based Robotics (MIT Press, 1998) ISBN 0-262-01165-4 Hendriks-Jansen, Horst (1996) Catching Ourselves in the Act: Situated Activity, Interactive Emergence, Evolution, and Human Thought. Cambridge, Mass.: MIT Press.

Concurrent MetateM

Concurrent MetateM is a multi-agent language in which each agent is programmed using a set of (augmented) temporal logic specifications of the behaviour it should exhibit. These specifications are executed directly to generate the behaviour of the agent. As a result, there is no risk of invalidating the logic as with systems where logical specification must first be translated to a lower-level implementation. The root of the MetateM concept is Gabbay's separation theorem; any arbitrary temporal logic formula can be rewritten in a logically equivalent past → future form. Execution proceeds by a process of continually matching rules against a history, and firing those rules when antecedents are satisfied. Any instantiated future-time consequents become commitments which must subsequently be satisfied, iteratively generating a model for the formula made up of the program rules. == Temporal Connectives == The Temporal Connectives of Concurrent MetateM can divided into two categories, as follows: Strict past time connectives: '●' (weak last), '◎' (strong last), '◆' (was), '■' (heretofore), 'S' (since), and 'Z' (zince, or weak since). Present and future time connectives: '◯' (next), '◇' (sometime), '□' (always), 'U' (until), and 'W' (unless). The connectives {◎,●,◆,■,◯,◇,□} are unary; the remainder are binary. === Strict past time connectives === ==== Weak last ==== ●ρ is satisfied now if ρ was true in the previous time. If ●ρ is interpreted at the beginning of time, it is satisfied despite there being no actual previous time. Hence "weak" last. ==== Strong last ==== ◎ρ is satisfied now if ρ was true in the previous time. If ◎ρ is interpreted at the beginning of time, it is not satisfied because there is no actual previous time. Hence "strong" last. ==== Was ==== ◆ρ is satisfied now if ρ was true in any previous moment in time. ==== Heretofore ==== ■ρ is satisfied now if ρ was true in every previous moment in time. ==== Since ==== ρSψ is satisfied now if ψ is true at any previous moment and ρ is true at every moment after that moment. ==== Zince, or weak since ==== ρZψ is satisfied now if (ψ is true at any previous moment and ρ is true at every moment after that moment) OR ψ has not happened in the past. === Present and future time connectives === ==== Next ==== ◯ρ is satisfied now if ρ is true in the next moment in time. ==== Sometime ==== ◇ρ is satisfied now if ρ is true now or in any future moment in time. ==== Always ==== □ρ is satisfied now if ρ is true now and in every future moment in time. ==== Until ==== ρUψ is satisfied now if ψ is true at any future moment and ρ is true at every moment prior. ==== Unless ==== ρWψ is satisfied now if (ψ is true at any future moment and ρ is true at every moment prior) OR ψ does not happen in the future.

Relational data mining

Relational data mining is the data mining technique for relational databases. Unlike traditional data mining algorithms, which look for patterns in a single table (propositional patterns), relational data mining algorithms look for patterns among multiple tables (relational patterns). For most types of propositional patterns, there are corresponding relational patterns. For example, there are relational classification rules (relational classification), relational regression tree, and relational association rules. There are several approaches to relational data mining: Inductive Logic Programming (ILP) Statistical Relational Learning (SRL) Graph Mining Propositionalization Multi-view learning == Algorithms == Multi-Relation Association Rules: Multi-Relation Association Rules (MRAR) is a new class of association rules which in contrast to primitive, simple and even multi-relational association rules (that are usually extracted from multi-relational databases), each rule item consists of one entity but several relations. These relations indicate indirect relationship between the entities. Consider the following MRAR where the first item consists of three relations live in, nearby and humid: “Those who live in a place which is near by a city with humid climate type and also are younger than 20 -> their health condition is good”. Such association rules are extractable from RDBMS data or semantic web data. == Software == Safarii: a Data Mining environment for analysing large relational databases based on a multi-relational data mining engine. Dataconda: a software, free for research and teaching purposes, that helps mining relational databases without the use of SQL. == Datasets == Relational dataset repository: a collection of publicly available relational datasets.

Jaggaer

JAGGAER, formerly SciQuest, is a provider of cloud-based business automation technology for Business Spend Management. Its headquarters is in Durham, North Carolina. == Company history == SciQuest was established in 1995 as a B2B eCommerce exchange.The company went public with an IPO in 1999. In 2001, SciQuest transitioned from a B2B exchange company into eProcurement software and supplier enablement platforms. SciQuest was taken private in 2004 and continued to move into eProcurement, inventory management and accounts payable automation. SciQuest completed an IPO in September 2010, raising approximately $57 million. SciQuest, and its 510 person workforce, was taken private in June 2016 as part of a $509 million acquisition by Accel-KKR, a private equity firm headquartered in Menlo Park, CA. In 2017 SciQuest was rebranded as JAGGAER and announced increased focus on offering a complete, integrated source-to-pay suite. Along with the name change, the company expanded its market focus to manufacturing, healthcare, consumer packaged goods, retail, education, life sciences, logistics and the public sector. JAGGAER acquired the European direct materials procurement specialist Pool4Tool in June 2017 giving it end-to-end direct as well as indirect materials procurement coverage. JAGGAER acquired spend management company BravoSolution in 2017, and entered into a joint venture with United Arab Emirates-based Tejari. In February 2019 JAGGAER launched JAGGAER One, which unifies its full product suite on a single platform. In 2019 the UK-based private equity firm Cinven acquired a majority holding in the company. Jim Bureau was subsequently named JAGGAER's Chief Executive Officer. Bureau left the firm in March 2023, and Andy Hovancik was announced as the company's CEO in June. In 2024, JAGGAER was acquired by Vista Equity Partners, a private equity firm specializing in enterprise software investments. == Current positioning == As of April 2025, JAGGAER positions itself as "an enterprise procurement and supplier collaboration SaaS provider." Its core technology platform, which is called JAGGAER One, serves "direct and indirect procurement with specializations in Higher Education, Discrete and Process Manufacturing, and Public Sector." == Product Categories == The JAGGAER One platform supports the following products: Spend Analytics Category Management Supplier Management Sourcing Contracts eProcurement Invoicing Inventory Management Supply Chain Collaboration Quality Management == Acquisitions == SciQuest acquired the following companies: AECsoft - January 2011. Provider of supplier management and sourcing technology. Upside Software, Inc. - August 2012. Provider of contract lifecycle management (CLM) solutions. Spend Radar, LLC - October 2012, Provider of spend analysis software. CombineNet - September 2013, Provider of advanced sourcing software JAGGAER acquired the following companies: POOL4TOOL - June 2017, Provider of direct sourcing and supply chain management software BravoSolution - December 2017, Provider of global platform spend management solutions

ASR-complete

ASR-complete is, by analogy to "NP-completeness" in complexity theory, a term to indicate that the difficulty of a computational problem is equivalent to solving the central automatic speech recognition problem, i.e. recognize and understanding spoken language. Unlike "NP-completeness", this term is typically used informally. Such problems are hypothesised to include: Spoken natural language understanding Understanding speech from far-field microphones, i.e. handling the reverbation and background noise These problems are easy for humans to do (in fact, they are described directly in terms of imitating humans). Some systems can solve very simple restricted versions of these problems, but none can solve them in their full generality.