ilastik is free open source software for image classification and segmentation. No previous experience in image processing is required to run the software. Since 2018 ilastik is further developed and maintained by Anna Kreshuk's group at European Molecular Biology Laboratory. == Features == ilastik allows user to annotate an arbitrary number of classes in images with a mouse interface. Using these user annotations and the generic (nonlinear) image features, the user can train a random forest classifier. Trained ilastik classifiers can be applied new data not included in the training set in ilastik via its batch processing functionality, or without using the graphical user interface, in headless mode. ilastik can be integrated into various related tools: Pre-trained workflows can be executed directly from ImageJ/Fiji using the ilastik-ImageJ plugin. Pre-trained ilastik Pixel Classification workflows can be run directly in Python with the ilastik Python package, which is available via conda. ilastik has a CellProfiler module to use ilastik classifiers to process images within a CellProfiler framework. == History == ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg. == Application == The Interactive Learning and Segmentation Toolkit Carving Cell classification and neuron classification Synapse detection Cell tracking Neural Network Classification == Resources == ilastik project is hosted on GitHub. It is a collaborative project, any contributions such as comments, bug reports, bug fixes or code contributions are welcome. The ilastik team can be contacted for user support on the image.sc forum.
Confused deputy problem
In information security, a confused deputy is a computer program that is tricked by another program (with fewer privileges or less rights) into misusing its authority on the system. It is a specific type of privilege escalation. The confused deputy problem is often cited as an example of why capability-based security is important. Capability systems protect against the confused deputy problem, whereas access-control list–based systems do not. Such systems can mitigate the confused deputy problem by eliminating ambient authority, allowing programs to act only on resources for which they hold explicit capabilities, whereas access-control list–based systems are more susceptible to it. However, this protection depends on correct implementation; in formally verified capability systems such as seL4, it can be shown that the kernel enforces capability constraints correctly, preventing such behavior at the system level. == Example == In the original example of a confused deputy, there was a compiler program provided on a commercial timesharing service. Users could run the compiler and optionally specify a filename where it would write debugging output, and the compiler would be able to write to that file if the user had permission to write there. The compiler also collected statistics about language feature usage. Those statistics were stored in a file called "(SYSX)STAT", in the directory "SYSX". To make this possible, the compiler program was given permission to write to files in SYSX. But there were other files in SYSX: in particular, the system's billing information was stored in a file "(SYSX)BILL". A user ran the compiler and named "(SYSX)BILL" as the desired debugging output file. This produced a confused deputy problem. The compiler made a request to the operating system to open (SYSX)BILL. Even though the user did not have access to that file, the compiler did, so the open succeeded. The compiler wrote the compilation output to the file (here "(SYSX)BILL") as normal, overwriting it, and the billing information was destroyed. === The confused deputy === In this example, the compiler program is the deputy because it is acting at the request of the user. The program is seen as 'confused' because it was tricked into overwriting the system's billing file. Whenever a program tries to access a file, the operating system needs to know two things: which file the program is asking for, and whether the program has permission to access the file. In the example, the file is designated by its name, “(SYSX)BILL”. The program receives the file name from the user, but does not know whether the user had permission to write the file. When the program opens the file, the system uses the program's permission, not the user's. When the file name was passed from the user to the program, the permission did not go along with it; the permission was increased by the system silently and automatically. It is not essential to the attack that the billing file be designated by a name represented as a string. The essential points are that: the designator for the file does not carry the full authority needed to access the file; the program's own permission to access the file is used implicitly. == Other examples == A cross-site request forgery (CSRF) is an example of a confused deputy attack that uses the web browser to perform sensitive actions against a web application. A common form of this attack occurs when a web application uses a cookie to authenticate all requests transmitted by a browser. Using JavaScript, an attacker can force a browser into transmitting authenticated HTTP requests. The Samy computer worm used cross-site scripting (XSS) to turn the browser's authenticated MySpace session into a confused deputy. Using XSS the worm forced the browser into posting an executable copy of the worm as a MySpace message which was then viewed and executed by friends of the infected user. Clickjacking is an attack where the user acts as the confused deputy. In this attack a user thinks they are harmlessly browsing a website (an attacker-controlled website) but they are in fact tricked into performing sensitive actions on another website. An FTP bounce attack can allow an attacker to connect indirectly to TCP ports to which the attacker's machine has no access, using a remote FTP server as the confused deputy. Another example relates to personal firewall software. It can restrict Internet access for specific applications. Some applications circumvent this by starting a browser with instructions to access a specific URL. The browser has authority to open a network connection, even though the application does not. Firewall software can attempt to address this by prompting the user in cases where one program starts another which then accesses the network. However, the user frequently does not have sufficient information to determine whether such an access is legitimate—false positives are common, and there is a substantial risk that even sophisticated users will become habituated to clicking "OK" to these prompts. Not every program that misuses authority is a confused deputy. Sometimes misuse of authority is simply a result of a program error. The confused deputy problem occurs when the designation of an object is passed from one program to another, and the associated permission changes unintentionally, without any explicit action by either party. It is insidious because neither party did anything explicit to change the authority. Another example is when an administrator authorizes an AI agent to act on their behalf, and that AI subsequently delegates authority to another AI agent neither vetted nor authorized by the original administrator. The unvetted AI can then act without permissions or oversight from the original developer. == Solutions == In some systems it is possible to ask the operating system to open a file using the permissions of another client. This solution has some drawbacks: It requires explicit attention to security by the server. A naive or careless server might not take this extra step. It becomes more difficult to identify the correct permission if the server is in turn the client of another service and wants to pass along access to the file. It requires the client to trust the server to not abuse the borrowed permissions. Note that intersecting the server and client's permissions does not solve the problem either, because the server may then have to be given very wide permissions (all of the time, rather than those needed for a given request) in order to act for arbitrary clients. The simplest way to solve the confused deputy problem is to bundle together the designation of an object and the permission to access that object. This is exactly what a capability is. Using capability security in the compiler example, the client would pass to the server a capability to the output file, such as a file descriptor, rather than the name of the file. Since it lacks a capability to the billing file, it cannot designate that file for output. In the cross-site request forgery example, a URL supplied "cross"-site would include its own authority independent of that of the client of the web browser.
Outline of brain mapping
The following outline is provided as an overview of and topical guide to brain mapping: Brain mapping – set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the (human or non-human) brain resulting in maps. Brain mapping is further defined as the study of the anatomy and function of the brain and spinal cord through the use of imaging (including intra-operative, microscopic, endoscopic and multi-modality imaging), immunohistochemistry, molecular and optogenetics, stem cell and cellular biology, engineering (material, electrical and biomedical), neurophysiology and nanotechnology. == Broad scope == History of neuroscience History of neurology Brain mapping Human brain Neuroscience Nervous system. === The neuron doctrine === Neuron doctrine – A set of carefully constructed elementary set of observations regarding neurons. For more granularity, more current, and more advanced topics, see the cellular level section Asserts that neurons fall under the broader cell theory, which postulates: All living organisms are composed of one or more cells. The cell is the basic unit of structure, function, and organization in all organisms. All cells come from preexisting, living cells. The Neuron doctrine postulates several elementary aspects of neurons: The brain is made up of individual cells (neurons) that contain specialized features such as dendrites, a cell body, and an axon. Neurons are cells differentiable from other tissues in the body. Neurons differ in size, shape, and structure according to their location or functional specialization. Every neuron has a nucleus, which is the trophic center of the cell (The part which must have access to nutrition). If the cell is divided, only the portion containing the nucleus will survive. Nerve fibers are the result of cell processes and the outgrowths of nerve cells. (Several axons are bound together to form one nerve fibril. See also: Neurofilament. Several nerve fibrils then form one large nerve fiber. Myelin, an electrical insulator, forms around selected axons. Neurons are generated by cell division. Neurons are connected by sites of contact and not via cytoplasmic continuity. (A cell membrane isolates the inside of the cell from its environment. Neurons do not communicate via direct cytoplasm to cytoplasm contact.) Law of dynamic polarization. Although the axon can conduct in both directions, in tissue there is a preferred direction of transmission from cell to cell. Elements added later to the initial Neuron doctrine A barrier to transmission exists at the site of contact between two neurons that may permit transmission. (Synapse) Unity of transmission. If a contact is made between two cells, then that contact can be either excitatory or inhibitory, but will always be of the same type. Dale's law, each nerve terminal releases a single type of neurotransmitter. Some of the basic postulates in the Neuron doctrine have been subsequently questioned, refuted, or updated. See the cellular level section topics for additional information. === Map, atlas, and database projects === Brain Activity Map Project – 2013 NIH $3 billion project to map every neuron in the human brain in ten years, based upon the Human Genome Project. NIH Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative [1] Community outreach site for above where the public may comment [2] Human Brain Project (EU) – 1 billion euro, 10-year project to simulate the human brain with supercomputers. BigBrain A high-resolution 3D atlas of the human brain created as part of the HBP. Human Connectome Project – 2009 NIH $30 million project to build a network map of the human brain, including structural (anatomical) and functional elements. Emphasis included research into dyslexia, autism, Alzheimer's disease, and schizophrenia. See also Connectome a, comprehensive map of neural connections in the brain. Allen Brain Atlas – 2003 $100 million project funded by Paul Allen (Microsoft) BrainMaps – National Institute of Health (NIH) database including 60 terabytes of image scans of primate and non-primates, integrated with information covering structure and function. NeuroNames – Defines the brain in terms of about 550 primary structures (about 850 unique structures) to which all other structures, names, and synonyms are related. About 15,000 neuroanatomical terms are cross indexed, including many synonyms in seven languages. Coverage includes the brain and spinal cord of the four species most frequently studied by neuroscientists: human, macaque (monkey), rat and mouse. The controlled, standardized vocabulary for each structure is located in an unambiguous, strict physical hierarchy, and these terms are selected based on ease of pronunciation, mnemonic value, and frequency of use in recent neuroscientific publications. Relation of each structure to its superstructures and substructures is included. The controlled vocabulary is suitable for uniquely indexing neuroanatomical information in digital databases. Decade of the Brain 1990–1999 promotion by NIH and the Library of Congress "to enhance public awareness of the benefits to be derived from brain research". Communications targeted Members of Congress, staffs, and the general public to promote funding. Talairach Atlas see Jean Talairach Harvard Whole Brain Atlas see Human brain MNI Template see Medical image computing Blue Brain Project and Artificial brain International Consortium for Brain Mapping see Brain Mapping List of neuroscience databases NIH Toolbox National Institute of Health (USA) toolbox for the assessment of neurological and behavioral function Organization for Human Brain Mapping The Organization for Human Brain Mapping (OHBM) is an international society dedicated to using neuroimaging to discover the organization of the human brain. == Imaging and recording systems == This section covers imaging and recording systems. The general section covers history, neuroimaging, and techniques for mapping specific neural connections. The specific systems section covers the various specific technologies, including experimental and widely deployed imaging and recording systems. === General === Most imaging work to date on individual neurons has been conducted outside the brain, typically on large neurons, and has been most frequently destructive. New techniques are however rapidly emerging. Search on "Single neuron imaging" and see related topics: Biological neuron model, Single-unit recording, Neural oscillation, Computational neuroscience. dMRI (above) is also promising in non-destructive imaging of single neurons inside the brain. History of neuroimaging (redirects from Brain scanner) Neuroimaging (redirects from Brain function map) Connectomics – mapping technique showing neural connections in a nervous system. === Specific systems === Cortical stimulation mapping Diffusion MRI (dMRI) – includes diffusion tensor imaging (DTI) and diffusion functional MRI (DfMRI). dMRI is a recent breakthrough in brain mapping allowing the visualization of cross connections between different anatomical parts of the brain. It allows noninvasive imaging of white matter fiber structure and in addition to mapping can be useful in clinical observations of abnormalities, including damage from stroke. Electroencephalography (EEG) – uses electrodes on the scalp and other techniques to detect the electrical flow of currents. Electrocorticography – intracranial EEG, the practice of using electrodes placed directly on the exposed surface of the brain to record electrical activity from the cerebral cortex. Electrophysiological techniques for clinical diagnosis Functional magnetic resonance imaging (fMRI) Medical image computing (brain research of leads medical and surgical uses of mapping technology) Neurostimulation (in research stimulation is frequently used in conjunction with imaging) Positron emission tomography (PET) – a nuclear medical imaging technique that produces a three-dimensional image or picture of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. Three-dimensional images of tracer concentration within the body are then constructed by computer analysis. In modern scanners, three dimensional imaging is often accomplished with the aid of a CT X-ray scan performed on the patient during the same session, in the same machine. === Imaging and recording componentry === ==== Electrochemical ==== Haemodynamic response – the rapid delivery of blood to active neuronal tissues. Blood Oxygenation Level Dependent signal (BOLD), corresponds to the concentration of deoxyhemoglobin. The BOLD effect is based on the fact that when neuronal activity is increased in one part of the brain, there is also an increased amount of cerebral blood flow to that area. Functional m
Content Security Policy
Content Security Policy (CSP) is a computer security standard introduced to prevent cross-site scripting (XSS), clickjacking and other code injection attacks resulting from execution of malicious content in the trusted web page context. It is a Candidate Recommendation of the W3C working group on Web Application Security, widely supported by modern web browsers. CSP provides a standard method for website owners to declare approved origins of content that browsers should be allowed to load on that website—covered types are JavaScript, CSS, HTML frames, web workers, fonts, images, embeddable objects such as Java applets, ActiveX, audio and video files, and other HTML5 features. == Status == The standard, originally named Content Restrictions, was proposed by Robert Hansen in 2004, first implemented in Firefox 4 and quickly picked up by other browsers. Version 1 of the standard was published in 2012 as W3C candidate recommendation and quickly with further versions (Level 2) published in 2014. As of 2023, the draft of Level 3 is being developed with the new features being quickly adopted by the web browsers. The following header names are in use as part of experimental CSP implementations: Content-Security-Policy – standard header name proposed by the W3C document. Google Chrome supports this as of version 25. Firefox supports this as of version 23, released on 6 August 2013. WebKit supports this as of version 528 (nightly build). Chromium-based Microsoft Edge support is similar to Chrome's. X-WebKit-CSP – deprecated, experimental header introduced into Google Chrome, Safari and other WebKit-based web browsers in 2011. X-Content-Security-Policy – deprecated, experimental header introduced in Gecko 2 based browsers (Firefox 4 to Firefox 22, Thunderbird 3.3, SeaMonkey 2.1). A website can declare multiple CSP headers, also mixing enforcement and report-only ones. Each header will be processed separately by the browser. CSP can also be delivered within the HTML code using a meta tag, although in this case its effectiveness will be limited. Internet Explorer 10 and Internet Explorer 11 also support CSP, but only sandbox directive, using the experimental X-Content-Security-Policy header. A number of web application frameworks support CSP, for example AngularJS (natively) and Django (middleware). Instructions for Ruby on Rails have been posted by GitHub. Web framework support is however only required if the CSP contents somehow depend on the web application's state—such as usage of the nonce origin. Otherwise, the CSP is rather static and can be delivered from web application tiers above the application, for example on load balancer or web server. === Bypasses === In December 2015 and December 2016, a few methods of bypassing 'nonce' allowlisting origins were published. In January 2016, another method was published, which leverages server-wide CSP allowlisting to exploit old and vulnerable versions of JavaScript libraries hosted at the same server (frequent case with CDN servers). In May 2017 one more method was published to bypass CSP using web application frameworks code. == Mode of operation == If the Content-Security-Policy header is present in the server response, a compliant client enforces the declarative allowlist policy. One example goal of a policy is a stricter execution mode for JavaScript in order to prevent certain cross-site scripting attacks. In practice this means that a number of features are disabled by default: Inline JavaScript code