Underwater computer vision is a subfield of computer vision. In recent years, with the development of underwater vehicles ( ROV, AUV, gliders), the need to be able to record and process huge amounts of information has become increasingly important. Applications range from inspection of underwater structures for the offshore industry to the identification and counting of fishes for biological research. However, no matter how big the impact of this technology can be to industry and research, it still is in a very early stage of development compared to traditional computer vision. One reason for this is that, the moment the camera goes into the water, a whole new set of challenges appear. On one hand, cameras have to be made waterproof, marine corrosion deteriorates materials quickly and access and modifications to experimental setups are costly, both in time and resources. On the other hand, the physical properties of the water make light behave differently, changing the appearance of a same object with variations of depth, organic material, currents, temperature etc. == Applications == Seafloor survey Vehicle navigation and positioning Biological monitoring {possibly aquatic biomonitoring) Video mosaics as visual navigation maps Submarine pipeline inspection Wreckage visualization Maintenance of underwater structures Drowning detection systems == Medium differences == === Illumination === In air, light comes from the whole hemisphere on cloudy days, and is dominated by the sun. In water direct lighting comes from a cone about 96° wide above the scene. This phenomenon is called Snell's window. Artificial lighting can be used where natural light levels are insufficient and where the light path is too long to produce acceptable colour, as the loss of colour is a function of the total distance through water from the source to the camera lens port. === Light attenuation === Unlike air, water attenuates light exponentially. This results in hazy images with very low contrast. The main reasons for light attenuation are light absorption (where energy is removed from the light) and light scattering, by which the direction of light is changed. Light scattering can further be divided into forward scattering, which results in an increased blurriness and backward scattering that limits the contrast and is responsible for the characteristic veil of underwater images. Both scattering and attenuation are heavily influenced by the amount of organic matter dissolved or suspended in the water. Light attenuation in water is also a function of the wavelength. This means that different colours are attenuated at different rates, leading to colour degradation.with depth and distance. Red and orange light are attenuated faster, followed by yellows and greens. Blue is the least attenuated visible wavelength. === Artificial lighting === == Challenges == In high level computer vision, human structures are frequently used as image features for image matching in different applications. However, the sea bottom lacks such features, making it hard to find correspondences in two images. In order to be able to use a camera in the water, a watertight housing is required. However, refraction will happen at the water-glass and glass-air interface due to differences in density of the materials. This has the effect of introducing a non-linear image deformation. The motion of the vehicle presents another special challenge. Underwater vehicles are constantly moving due to currents and other phenomena. This introduces another uncertainty to algorithms, where small motions may appear in all directions. This can be specially important for video tracking. In order to reduce this problem image stabilization algorithms may be applied. == Relevant technology == === Image restoration === Image restoration< techniques are intended to model the degradation process and then invert it, obtaining the new image after solving. It is generally a complex approach that requires plenty of parameters that vary a lot between different water conditions. === Image enhancement === Image enhancement only tries to provide a visually more appealing image without taking the physical image formation process into account. These methods are usually simpler and less computational intensive. === Color correction === Various algorithms exist that perform automatic color correction. The UCM (Unsupervised Color Correction Method), for example, does this in the following steps: It firstly reduces the color cast by equalizing the color values. Then it enhances contrast by stretching the red histogram towards the maximum and finally saturation and intensity components are optimized. == Underwater stereo vision == It is usually assumed that stereo cameras have been calibrated previously, geometrically and radiometrically. This leads to the assumption that corresponding pixels should have the same color. However this can not be guaranteed in an underwater scene, because of dispersion and backscatter. However, it is possible to digitally model this phenomenon and create a virtual image with those effects removed == Other application fields == Imaging sonars have become more and more accessible and gained resolution, delivering better images. Sidescan sonars are used to produce complete maps of regions of the sea floor stitching together sequences of sonar images. However, sonar images often lack proper contrast and are degraded by artefacts and distortions due to noise, attitude changes of the AUV/ROV carrying the sonar or non uniform beam patterns. Another common problem with sonar computer vision is the comparatively low frame rate of sonar images.
Biopython
Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe. Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis. == History == The development of Biopython began in 1999, and it was first released in July 2000. First "semi-complete" and "semi-stable" release was done in March 2001 and December 2002 respectively. It was developed during a similar time frame and with analogous goals to other projects that added bioinformatics capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew Dalke and Brad Chapman, though over 100 people have made contributions to date. In 2007, a similar Python project, namely PyCogent, was established. The initial scope of Biopython involved accessing, indexing and processing biological sequence files. The retrieved data from common biological databases will then be parsed into a python data structure. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology. The key challenge in the design of parsers for bioinformatics file formats is the frequency at which the data formats change. This is due to inadequate curation of the structure of the data, and changes in the database contents. This problem is overcome by the application of a standard event-oriented parser design (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. The current stable release of Biopython version 1.85 was released on 15 January 2025. It only supports Python 3 and the recent releases of Biopython require NumPy (and not Numeric). == Design == Wherever possible, Biopython follows the conventions used by the Python programming language to make it easier for users familiar with Python. For example, Seq and SeqRecord objects can be manipulated via slicing, in a manner similar to Python's strings and lists. It is also designed to be functionally similar to other Bio projects, such as BioPerl. It is organized into modular sub-packages, e.g., Bio.Seq, Bio.Align, Bio.PDB, Bio.Entrez each of them useful in a different bioinformatics domain. It used principles, like encapsulation and polymorphism, notably in classes Seq, SeqRecord, and Bio.PDB.Structure. It can also interoperate with other Python tools (Pandas, Matplotlib and SciPy). Biopython can read and write most common file formats for each of its functional areas, and its license is permissive and compatible with most other software licenses, which allows Biopython to be used in a variety of software projects. == Requirements == Biopython is currently supported and tested with the following Python implementations: Python 3 or PyPy3 NumPy == Key features and examples == === Input and output === Biopython can read and write to a number of common formats. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others. Very large sequence files can exceed a computer's memory resources, so Biopython provides various options for accessing records in large files. They can be loaded entirely into memory in Python data structures, such as lists or dictionaries, providing fast access at the cost of memory usage. Alternatively, the files can be read from disk as needed, with slower performance but lower memory requirements. === Sequences === A core concept in Biopython is the biological sequence, and this is represented by the Seq class. A Biopython Seq object is similar to a Python string in many respects: it supports the Python slice notation, can be concatenated with other sequences and is immutable. This object includes both general string-like and biological sequence-specific methods. It is best to store information about the biological type (DNA, RNA, protein) separately from the sequence, rather than using an explicit alphabet argument. === Sequence annotation === The SeqRecord class describes sequences, along with information such as name, description and features in the form of SeqFeature objects. Each SeqFeature object specifies the type of the feature and its location. Feature types can be ‘gene’, ‘CDS’ (coding sequence), ‘repeat_region’, ‘mobile_element’ or others, and the position of features in the sequence can be exact or approximate. === Accessing online databases === Through the Bio.Entrez module, users of Biopython can download biological data from NCBI databases. Each of the functions provided by the Entrez search engine is available through functions in this module, including searching for and downloading records. === Phylogeny === The Bio.Phylo module provides tools for working with and visualising phylogenetic trees. A variety of file formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and Clade objects. Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score. Rooted trees can be drawn in ASCII or using matplotlib (see Figure 1), and the Graphviz library can be used to create unrooted layouts (see Figure 2). === Genome diagrams === The GenomeDiagram module provides methods of visualising sequences within Biopython. Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including PDF and PNG. Diagrams are created by making tracks and then adding sequence features to those tracks. By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram. Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram. === Macromolecular structure === The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain Atom objects. Disordered residues and atoms get their own classes, DisorderedResidue and DisorderedAtom, that describe their uncertain positions. Using Bio.PDB, one can navigate through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring distances or angles, comparing residues and calculating residue depth. === Population genetics === The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program. === Wrappers for command line tools === Biopython previously included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the code using specialized Biopython classes. However, Bio.Application modules and their wrappers have deprecated and will be removed in future Biopython releases. The main reason for this is the high maintenance burden of updating them with the evolving external tools. The recommended approach is to directly construct and execute command-line tool commands using Python’s built-in subprocess module. This method provides flexibility and removes the dependency on the Biopython wrappers. subprocess is a native Python module useful for running ext
Bring your own encryption
Bring your own encryption (BYOE), also known as bring your own key (BYOK), is a cloud computing security model that allows cloud service customers to use their own encryption software and manage their own encryption keys. == Overview == BYOE enables cloud service customers to utilize a virtual instance of their encryption software alongside their cloud-hosted business applications to encrypt their data. In this model, hosted business applications are configured to process all data through the encryption software. This software then writes the ciphertext version of the data to the cloud service provider's physical data store and decrypts ciphertext data upon retrieval requests. This approach provides enterprises with control over their keys and the ability to generate their own master key using internal hardware security modules (HSM), which are then transmitted to the cloud provider's HSM. When the data is no longer needed, such as when users discontinue the cloud service, the keys can be deleted, rendering the encrypted data permanently inaccessible. This practice is known as crypto-shredding. == Potential Advantages == Organizations can store data with unique encryption that only they can access. Multiple organizations can share the same hardware infrastructure via cloud services like Amazon Web Services (AWS) or Google Cloud while maintaining encryption to comply with regulations such as HIPAA. == Potential Challenges == Resource utilization may be higher compared to traditional encryption practices when multiple users share the same hardware and use their own encryption. Efforts to minimize resource utilization issues may potentially impact security benefits.
Google Gadgets
Google Gadgets are dynamic web content that can be embedded on a web page. They can be added to and interact strongly with Google's iGoogle personalized home page (discontinued in November 2013, although iGoogle Gadgets still work on other websites) and the Google Desktop (discontinued in September 2011) application, as well as Google Wave (also no longer supported by Google) and Google Sites. Webmasters can add and customize a gadget to their own business or personal web site, a process called "syndication". Gadgets are developed by Google and third-party developers using the Google Gadgets API, using basic web technologies such as XML and JavaScript. == Multi-user persistent - Wave Gadgets == With the advent of Google Wave (now Apache Wave), gadgets became able to have persistent storage and multi-user capabilities and better state management. Gadgets using Google Wave in this way were simply known as 'Wave Gadgets'. For instance, a game written using a Google Gadget could use Google Wave technology to record a list of users and high scores without having to worry about how to permanently store the scores on a hosted server. The use of Google Wave would give the gadget multi-user and permanent storage capabilities. For example, scores could be stored in a Google Wave hosted permanently by Google at no cost to the user. As of early 2013, Google Gadgets were deprecated in Google Spreadsheets. Shortly after, they were removed from all spreadsheets. == Technology == Google Gadgets are written in XML and can have HTML and JavaScript components, and were able to use Google Wave. Here is an example of a Hello World program written using Google Gadget technology. Google Gadgets API is a Google API which allows developers to create Google Gadgets easily.
Web-based simulation
Web-based simulation (WBS) is the invocation of computer simulation services over the World Wide Web, specifically through a web browser. Increasingly, the web is being looked upon as an environment for providing modeling and simulation applications, and as such, is an emerging area of investigation within the simulation community. == Application == Web-based simulation is used in several contexts: In e-learning, various principles can quickly be illustrated to students by means of interactive computer animations, for example during lecture demonstrations and computer exercises. In distance learning, web-based simulation may provide an alternative to installing expensive simulation software on the student computer, or an alternative to expensive laboratory equipment. In software engineering, web-based emulation allows application development and testing on one platform for other target platforms, for example for various mobile operating systems or mobile web browsers, without the need of target hardware or locally installed emulation software. In online computer games, 3D environments can be simulated, and old home computers and video game consoles can be emulated, allowing the user to play old computer games in the web browser. In medical education, nurse education and allied health education (like sonographer training), web-based simulations can be used for learning and practicing clinical healthcare procedures. Web-based procedural simulations emphasize the cognitive elements such as the steps of the procedure, the decisions, the tools/devices to be used, and the correct anatomical location. == Client-side vs server-side approaches == Web-based simulation can take place either on the server side or on the client side. In server-side simulation, the numerical calculations and visualization (generation of plots and other computer graphics) is carried out on the web server, while the interactive graphical user interface (GUI) often partly is provided by the client-side, for example using server-side scripting such as PHP or CGI scripts, interactive services based on Ajax or a conventional application software remotely accessed through a VNC Java applet. In client-side simulation, the simulation program is downloaded from the server side but completely executed on the client side, for example using Java applets, Flash animations, JavaScript, or some mathematical software viewer plug-in. Server-side simulation is not scalable for many simultaneous users, but places fewer demands on the user computer performance and web-browser plug-ins than client-side simulation. The term on-line simulation sometimes refers to server-side web-based simulation, sometimes to symbiotic simulation, i.e. a simulation that interacts in real-time with a physical system. The upcoming cloud-computing technologies can be used for new server-side simulation approaches. For instance, there are multi-agent-simulation applications which are deployed on cloud-computing instances and act independently. This allows simulations to be highly scalable. == Existing tools == AgentSheets – graphically programmed tool for creating web-based The Sims-like simulation games, and for teaching beginner students programming. AnyLogic – a graphically programmed tool that generates Java code for discrete-event simulation, system dynamics and agent-based models Easy Java Simulations – a tool for modelling and visualization of physical phenomenons, that automatically generates Java code from mathematical expressions. ExploreLearning Gizmos – a large library of interactive online simulations for math and science education in grades 3–12. FreeFem++ Javascript Version – FreeFem++ is a free and open source PDE solver using the finite element method. GNU Octave web interfaces – MATLAB compatible open-source software Lanner Group Ltd L-SIM Server – Java-based discrete-event simulation engine which supports model standards such as BPMN 2.0 Nanohub – web 2.0 in-browser interactive simulation of nanotechnology NetLogo – a multi-agent programming language and integrated modeling environment that runs on the Java Virtual Machine OpenPlaG – PHP-based function graph plotter for the use on websites OpenEpi – web-based packet of tools for biostatistics Recursive Porous Agent Simulation Toolkit (Repast) – agent-based modeling and simulation toolkit implemented in Java and many other languages SageMath – open-source numerical-analysis software with web interface, based on the Python programming language SimScale – web-based simulation platform supporting computational fluid dynamics, solid mechanics, and thermodynamics StarLogo – agent-based simulation language written in Java. VisSim viewer – graphically programmed data-flow diagrams for simulation of dynamical systems webMathematica and Mathematica Player – a computer algebra system and programming language. VisualSim Architect – VisualSim Explorer enables system-level models to be embedded in documents for viewing, simulation and analysis from within a web browser without any local software installation.
U-Net
U-Net is a convolutional neural network that was developed for image segmentation. The network is based on a fully convolutional neural network whose architecture was modified and extended to work with fewer training images and to yield more precise segmentation. Segmentation of a 512 × 512 image takes less than a second on a modern (2015) GPU using the U-Net architecture. The U-Net architecture has also been employed in diffusion models for iterative image denoising. This technology underlies many modern image generation models, such as DALL-E, Midjourney, and Stable Diffusion. U-Net is also being explored for language models. Tokenization is not a separate step, allowing the model to more easily understand spelling and concurrently vectorizing / tokenizing higher level concepts. == Description == The U-Net architecture stems from the so-called "fully convolutional network". The main idea is to supplement a usual contracting network by successive layers, where pooling operations are replaced by upsampling operators. Hence these layers increase the resolution of the output. A successive convolutional layer can then learn to assemble a precise output based on this information. One important modification in U-Net is that there are a large number of feature channels in the upsampling part, which allow the network to propagate context information to higher resolution layers. As a consequence, the expansive path is more or less symmetric to the contracting part, and yields a u-shaped architecture. The network only uses the valid part of each convolution without any fully connected layers. To predict the pixels in the border region of the image, the missing context is extrapolated by mirroring the input image. This tiling strategy is important to apply the network to large images, since otherwise the resolution would be limited by the GPU memory. Recently, there had also been an interest in receptive field based U-Net models for medical image segmentation. == Network architecture == The network consists of a contracting path and an expansive path, which gives it the u-shaped architecture. The contracting path is a typical convolutional network that consists of repeated application of convolutions, each followed by a rectified linear unit (ReLU) and a max pooling operation. During the contraction, the spatial information is reduced while feature information is increased. The expansive pathway combines the feature and spatial information through a sequence of up-convolutions and concatenations with high-resolution features from the contracting path. == Applications == There are many applications of U-Net in biomedical image segmentation, such as brain image segmentation (''BRATS'') and liver image segmentation ("siliver07") as well as protein binding site prediction. U-Net implementations have also found use in the physical sciences, for example in the analysis of micrographs of materials. Variations of the U-Net have also been applied for medical image reconstruction. Here are some variants and applications of U-Net as follows: Pixel-wise regression using U-Net and its application on pansharpening; 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation; TernausNet: U-Net with VGG11 Encoder Pre-Trained on ImageNet for Image Segmentation. Image-to-image translation to estimate fluorescent stains In binding site prediction of protein structure. == History == U-Net was created by Olaf Ronneberger, Philipp Fischer, Thomas Brox in 2015 and reported in the paper "U-Net: Convolutional Networks for Biomedical Image Segmentation". It is an improvement and development of FCN: Evan Shelhamer, Jonathan Long, Trevor Darrell (2014). "Fully convolutional networks for semantic segmentation".
Qstack
Qstack is a cloud management platform developed by GreenQloud, a cloud computing software company founded in Reykjavik, Iceland in February 2010. Qstack enables its users to manage multiple clouds and hybrid deployments through a single self-service portal. Qstack is in continuous development, incorporating developments within infrastructure, cloud, and application management solutions. The next release of Qstack is slated for June 2017. == History == In 2014 when Jonsi Stefansson joined as CEO, Greenqloud pivoted its operational focus to development of Qstack with beta launch in the fall of 2015, and began offering support, technical services and certifications for the software. == Features == Qstack is hypervisor agnostic (KVM, VMware, Hyper-V) and can manage private clouds in multiple locations as well as AWS, Azure, and EC2-compatible public clouds from its user interface. Qstack combines proprietary software with open-source components, and the company claims to harden them to meet the strict security standards often required by enterprise deployments. Qstack features VM templates for Windows, Linux, and other operating systems. It also features full SSH/RDP access to instances, virtual routers, firewalls, and load balancers built into the interface. == Reception == In a 2015 review, IDG columnist J. Peter Bruzzese praised Qstack’s user interface for its ease-of-use and clean look.