Microscope image processing is a broad term that covers the use of digital image processing techniques to process, analyze and present images obtained from a microscope. Such processing is now commonplace in a number of diverse fields such as medicine, biological research, cancer research, drug testing, metallurgy, etc. A number of manufacturers of microscopes now specifically design in features that allow the microscopes to interface to an image processing system. == Image acquisition == Until the early 1990s, most image acquisition in video microscopy applications was typically done with an analog video camera, often simply closed circuit TV cameras. While this required the use of a frame grabber to digitize the images, video cameras provided images at full video frame rate (25-30 frames per second) allowing live video recording and processing. While the advent of solid state detectors yielded several advantages, the real-time video camera was actually superior in many respects. Today, acquisition is usually done using a CCD camera mounted in the optical path of the microscope. The camera may be full colour or monochrome. Very often, very high resolution cameras are employed to gain as much direct information as possible. Cryogenic cooling is also common, to minimise noise. Often digital cameras used for this application provide pixel intensity data to a resolution of 12-16 bits, much higher than is used in consumer imaging products. Ironically, in recent years, much effort has been put into acquiring data at video rates, or higher (25-30 frames per second or higher). What was once easy with off-the-shelf video cameras now requires special, high speed electronics to handle the vast digital data bandwidth. Higher speed acquisition allows dynamic processes to be observed in real time, or stored for later playback and analysis. Combined with the high image resolution, this approach can generate vast quantities of raw data, which can be a challenge to deal with, even with a modern computer system. While current CCD detectors allow very high image resolution, often this involves a trade-off because, for a given chip size, as the pixel count increases, the pixel size decreases. As the pixels get smaller, their well depth decreases, reducing the number of electrons that can be stored. In turn, this results in a poorer signal-to-noise ratio. For best results, one must select an appropriate sensor for a given application. Because microscope images have an intrinsic limiting resolution, it often makes little sense to use a noisy, high resolution detector for image acquisition. A more modest detector, with larger pixels, can often produce much higher quality images because of reduced noise. This is especially important in low-light applications such as fluorescence microscopy. Moreover, one must also consider the temporal resolution requirements of the application. A lower resolution detector will often have a significantly higher acquisition rate, permitting the observation of faster events. Conversely, if the observed object is motionless, one may wish to acquire images at the highest possible spatial resolution without regard to the time required to acquire a single image. == 2D image techniques == Image processing for microscopy application begins with fundamental techniques intended to most accurately reproduce the information contained in the microscopic sample. This might include adjusting the brightness and contrast of the image, averaging images to reduce image noise and correcting for illumination non-uniformities. Such processing involves only basic arithmetic operations between images (i.e. addition, subtraction, multiplication and division). The vast majority of processing done on microscope image is of this nature. Another class of common 2D operations called image convolution are often used to reduce or enhance image details. Such "blurring" and "sharpening" algorithms in most programs work by altering a pixel's value based on a weighted sum of that and the surrounding pixels (a more detailed description of kernel based convolution deserves an entry for itself) or by altering the frequency domain function of the image using Fourier Transform. Most image processing techniques are performed in the Frequency domain. Other basic two dimensional techniques include operations such as image rotation, warping, color balancing etc. At times, advanced techniques are employed with the goal of "undoing" the distortion of the optical path of the microscope, thus eliminating distortions and blurring caused by the instrumentation. This process is called deconvolution, and a variety of algorithms have been developed, some of great mathematical complexity. The end result is an image far sharper and clearer than could be obtained in the optical domain alone. This is typically a 3-dimensional operation, that analyzes a volumetric image (i.e. images taken at a variety of focal planes through the sample) and uses this data to reconstruct a more accurate 3-dimensional image. == 3D image techniques == Another common requirement is to take a series of images at a fixed position, but at different focal depths. Since most microscopic samples are essentially transparent, and the depth of field of the focused sample is exceptionally narrow, it is possible to capture images "through" a three-dimensional object using 2D equipment like confocal microscopes. Software is then able to reconstruct a 3D model of the original sample which may be manipulated appropriately. The processing turns a 2D instrument into a 3D instrument, which would not otherwise exist. In recent times this technique has led to a number of scientific discoveries in cell biology. == Analysis == Analysis of images will vary considerably according to application. Typical analysis includes determining where the edges of an object are, counting similar objects, calculating the area, perimeter length and other useful measurements of each object. A common approach is to create an image mask which only includes pixels that match certain criteria, then perform simpler scanning operations on the resulting mask. It is also possible to label objects and track their motion over a series of frames in a video sequence.
Elements of AI
Elements of AI is a massive open online course (MOOC) teaching the basics of artificial intelligence. The course, originally launched in 2018, is designed and organized by the University of Helsinki and learning technology company MinnaLearn. The course includes modules on machine learning, neural networks, the philosophy of artificial intelligence, and using artificial intelligence to solve problems. It consists of two parts: Introduction to AI and its sequel, Building AI, that was released in late 2020. In November 2019, the course was named one of four winners of MIT’s Inclusive Innovation Challenge. University of Helsinki's computer science department is known as the alma mater of Linus Torvalds, a Finnish-American software engineer who is the creator of the Linux kernel, which is the kernel for Linux operating systems. == EU’s AI pledge == The government of Finland has pledged to offer the course for all EU citizens by the end of 2021, as the course is made available in all the official EU languages. The initiative was launched as part of Finland's Presidency of the Council of the European Union in 2019, with the European Commission providing translations of the course materials. In 2017, Finland launched an AI strategy to stay competitive in the field of AI amid growing competition between China and the United States. With the support of private companies and the government, Finland's now-realized goal was to get 1 percent of its citizens to participate in Elements of AI. Other governments have also given their support to the course. For instance, Germany's Federal Minister for Economic Affairs and Energy Peter Altmeier has encouraged citizens to take part in the course to help Germany gain a competitive advantage in AI. Sweden's Minister for Energy and Minister for Digital Development Anders Ygeman has said that Sweden aims to teach 1 percent of its population the basics of AI like Finland has. == Participants == Elements of AI had enrolled more than 1 million students from more than 110 countries by May 2023. A quarter of the course's participants are aged 45 and over, and some 40 percent are women. Among Nordic participants, the share of women is nearly 60 percent. In September 2022, the course was available in Finnish, Swedish, Estonian, English, German, Latvian, Norwegian, French, Belgian, Czech, Greek, Slovakian, Slovenian, Latvian, Lithuanian, Portuguese, Spanish, Irish, Icelandic, Maltese, Croatian, Romanian, Italian, Dutch, Polish, and Danish.
Personal knowledge base
A personal knowledge base (PKB) is an electronic tool used by an individual to express, capture, and later retrieve personal knowledge. It differs from a traditional database in that it contains subjective material particular to the owner, that others may not agree with nor care about. Importantly, a PKB consists primarily of knowledge, rather than information; in other words, it is not a collection of documents or other sources an individual has encountered, but rather an expression of the distilled knowledge the owner has extracted from those sources or from elsewhere. The term personal knowledge base was mentioned as early as the 1980s, but the term came to prominence in the 2000s when it was described at length in publications by computer scientist Stephen Davies and colleagues, who compared PKBs on a number of different dimensions, the most important of which is the data model that each PKB uses to organize knowledge. == Data models == Davies and colleagues examined three aspects of the data models of PKBs: their structural framework, which prescribes rules about how knowledge elements can be structured and interrelated (as a tree, graph, tree plus graph, spatially, categorically, as n-ary links, chronologically, or ZigZag); their knowledge elements, or basic building blocks of information that a user creates and works with, and the level of granularity of those knowledge elements (such as word/concept, phrase/proposition, free text notes, links to information sources, or composite); and their schema, which involves the level of formal semantics introduced into the data model (such as a type system and related schemas, keywords, attribute–value pairs, etc.). Davies and colleagues also emphasized the principle of transclusion, "the ability to view the same knowledge element (not a copy) in multiple contexts", which they considered to be "pivotal" to an ideal PKB. They concluded, after reviewing many design goals, that the ideal PKB was still to come in the future. === Personal knowledge graph === In their publications on PKBs, Davies and colleagues discussed knowledge graphs as they were implemented in some software of the time. Later, other writers used the term personal knowledge graph (PKG) to refer to a PKB featuring a graph structure and graph visualization. However, the term personal knowledge graph is also used by software engineers to refer to the different subject of a knowledge graph about a person, in contrast to a knowledge graph created by a person in a PKB. == Software architecture == Davies and colleagues also differentiated PKBs according to their software architecture: file-based, database-based, or client–server systems (including Internet-based systems accessed through desktop computers and/or handheld mobile devices). == History == Non-electronic personal knowledge bases have probably existed in some form for centuries: Leonardo da Vinci's journals and notes are a famous example of the use of notebooks. Commonplace books, florilegia, annotated private libraries, and card files (in German, Zettelkästen) of index cards and edge-notched cards are examples of formats that have served this function in the pre-electronic age. Undoubtedly the most famous early formulation of an electronic PKB was Vannevar Bush's description of the "memex" in 1945. In a 1962 technical report, human–computer interaction pioneer Douglas Engelbart (who would later become famous for his 1968 "Mother of All Demos" that demonstrated almost all the fundamental elements of modern personal computing) described his use of edge-notched cards to partially model Bush's memex. == Examples == The following software applications have been used to build PKBs using various data models and architectures. The list includes software mentioned by Davies and colleagues in their 2005 paper, and additional software. Open source Compendium Haystack (MIT project) Joplin Logseq NoteCards Org-mode QOwnNotes TiddlyWiki Closed source Evernote Microsoft OneNote MindManager MyLifeBits Notion Obsidian Personal Knowbase PersonalBrain Roam Tinderbox
Leabra
Leabra stands for local, error-driven and associative, biologically realistic algorithm. It is a model of learning which is a balance between Hebbian and error-driven learning with other network-derived characteristics. This model is used to mathematically predict outcomes based on inputs and previous learning influences. Leabra is heavily influenced by and contributes to neural network designs and models, including emergent. == Background == It is the default algorithm in emergent (successor of PDP++) when making a new project, and is extensively used in various simulations. Hebbian learning is performed using conditional principal components analysis (CPCA) algorithm with correction factor for sparse expected activity levels. Error-driven learning is performed using GeneRec, which is a generalization of the recirculation algorithm, and approximates Almeida–Pineda recurrent backpropagation. The symmetric, midpoint version of GeneRec is used, which is equivalent to the contrastive Hebbian learning algorithm (CHL). See O'Reilly (1996; Neural Computation) for more details. The activation function is a point-neuron approximation with both discrete spiking and continuous rate-code output. Layer or unit-group level inhibition can be computed directly using a k-winners-take-all (KWTA) function, producing sparse distributed representations. A feedforward and feedback (FFFB) form of inhibition has now replaced the KWTA form of inhibition. FFFB inhibition can be efficiently implemented by using the average excitatory input and activity levels in a given layer. The net input is computed as an average, not a sum, over connections, based on normalized, sigmoidally transformed weight values, which are subject to scaling on a connection-group level to alter relative contributions. Automatic scaling is performed to compensate for differences in expected activity level in the different projections. Documentation about this algorithm can be found in the book "Computational Explorations in Cognitive Neuroscience: Understanding the Mind by Simulating the Brain" published by MIT press. and in the Emergent Documentation Archived 2009-04-16 at the Wayback Machine == Overview of the leabra algorithm == The pseudocode for Leabra is given here, showing exactly how the pieces of the algorithm described in more detail in the subsequent sections fit together. Iterate over minus and plus phases of settling for each event. o At start of settling, for all units: - Initialize all state variables (activation, v_m, etc.). - Apply external patterns (clamp input in minus, input & output in plus). - Compute net input scaling terms (constants, computed here so network can be dynamically altered). - Optimization: compute net input once from all static activations (e.g., hard-clamped external inputs). o During each cycle of settling, for all non-clamped units: - Compute excitatory netinput (g_e(t), aka eta_j or net) -- sender-based optimization by ignoring inactives. - Compute kWTA inhibition for each layer, based on g_i^Q: Sort units into two groups based on g_i^Q: top k and remaining k+1 -> n. If basic, find k and k+1th highest If avg-based, compute avg of 1 -> k & k+1 -> n. Set inhibitory conductance g_i from g^Q_k and g^Q_k+1 - Compute point-neuron activation combining excitatory input and inhibition o After settling, for all units, record final settling activations as either minus or plus phase (y^-_j or y^+_j). After both phases update the weights (based on linear current weight values), for all connections: o Compute error-driven weight changes with CHL with soft weight bounding o Compute Hebbian weight changes with CPCA from plus-phase activations o Compute net weight change as weighted sum of error-driven and Hebbian o Increment the weights according to net weight change. == Implementations == Emergent Archived 2015-10-03 at the Wayback Machine is the original implementation of Leabra; its most recent implementation is written in Go. It was written chiefly by Dr. O'Reilly, but professional software engineers were recently hired to improve the existing codebase. This is the fastest implementation, suitable for constructing large networks. Although emergent has a graphical user interface, it is very complex and has a steep learning curve. If you want to understand the algorithm in detail, it will be easier to read non-optimized code. For this purpose, check out the MATLAB version. There is also an R version available, that can be easily installed via install.packages("leabRa") in R and has a short introduction to how the package is used. The MATLAB and R versions are not suited for constructing very large networks, but they can be installed quickly and (with some programming background) are easy to use. Furthermore, they can also be adapted easily. == Special algorithms == Temporal differences and general dopamine modulation. Temporal differences (TD) is widely used as a model of midbrain dopaminergic firing. Primary value learned value (PVLV). PVLV simulates behavioral and neural data on Pavlovian conditioning and the midbrain dopaminergic neurons that fire in proportion to unexpected rewards (an alternative to TD). Prefrontal cortex basal ganglia working memory (PBWM). PBWM uses PVLV to train prefrontal cortex working memory updating system, based on the biology of the prefrontal cortex and basal ganglia.
WordNet
WordNet is a lexical database of semantic relations between words that links words into semantic relations including synonyms, hyponyms, and meronyms. The synonyms are grouped into synsets with short definitions and usage examples. It can thus be seen as a combination and extension of a dictionary and thesaurus. Its primary use is in automatic text analysis and artificial intelligence applications. It was first created in the English language and the English WordNet database and software tools have been released under a BSD style license and are freely available for download. The latest official release from Princeton was released in 2011. Princeton currently has no plans to release any new versions due to staffing and funding issues. New versions are still being released annually through the Open English WordNet website. Until about 2024 an online version was previously available through wordnet.princeton.edu. That version of WordNet has been deprecated, but a new online version is available at en-word.net. There are now WordNets in more than 200 languages. == History and team members == WordNet was first created in 1985, in English only, in the Cognitive Science Laboratory of Princeton University under the direction of psychology professor George Armitage Miller. It was later directed by Christiane Fellbaum. The project was initially funded by the U.S. Office of Naval Research, and later also by other U.S. government agencies including the DARPA, the National Science Foundation, the Disruptive Technology Office (formerly the Advanced Research and Development Activity) and REFLEX. George Miller and Christiane Fellbaum received the 2006 Antonio Zampolli Prize for their work with WordNet. The Global WordNet Association is a non-commercial organization that provides a platform for discussing, sharing and connecting WordNets for all languages in the world. Christiane Fellbaum and Piek Th.J.M. Vossen are its co-presidents. == Database contents == The database contains 155,327 words organized in 175,979 synsets for a total of 207,016 word-sense pairs; in compressed form, it is about 12 megabytes in size. It includes the lexical categories nouns, verbs, adjectives and adverbs but ignores prepositions, determiners and other function words. Words from the same lexical category that are roughly synonymous are grouped into synsets, which include simplex words as well as collocations like "eat out" and "car pool." The different senses of a polysemous word form are assigned to different synsets. A synset's meaning is further clarified with a short defining gloss and one or more usage examples. An example adjective synset is: good, right, ripe – (most suitable or right for a particular purpose; "a good time to plant tomatoes"; "the right time to act"; "the time is ripe for great sociological changes") All synsets are connected by means of semantic relations. These relations, which are not all shared by all lexical categories, include: Nouns hypernym: Y is a hypernym of X if every X is a (kind of) Y (canine is a hypernym of dog) hyponym: Y is a hyponym of X if every Y is a (kind of) X (dog is a hyponym of canine) coordinate term: Y is a coordinate term of X if X and Y share a hypernym (wolf is a coordinate term of dog, and dog is a coordinate term of wolf) holonym: Y is a holonym of X if X is a part of Y (building is a holonym of window) meronym: Y is a meronym of X if Y is a part of X (window is a meronym of building) Verbs hypernym: the verb Y is a hypernym of the verb X if the activity X is a (kind of) Y (to perceive is an hypernym of to listen) troponym: the verb Y is a troponym of the verb X if the activity Y is doing X in some manner (to lisp is a troponym of to talk) entailment: the verb Y is entailed by the verb X if by doing X you must be doing Y (to sleep is entailed by to snore) coordinate term: the verb Y is a coordinate term of the verb X if X and Y share a hypernym (to lisp is a coordinate term of to yell, and to yell is a coordinate term of to lisp) These semantic relations hold among all members of the linked synsets. Individual synset members (words) can also be connected with lexical relations. For example, (one sense of) the noun "director" is linked to (one sense of) the verb "direct" from which it is derived via a "morphosemantic" link. The morphology functions of the software distributed with the database try to deduce the lemma or stem form of a word from the user's input. Irregular forms are stored in a list, and looking up "ate" will return "eat," for example. == Knowledge structure == Both nouns and verbs are organized into hierarchies, defined by hypernym or IS A relationships. For instance, one sense of the word dog is found following hypernym hierarchy; the words at the same level represent synset members. Each set of synonyms has a unique index. At the top level, these hierarchies are organized into 25 beginner "trees" for nouns and 15 for verbs (called lexicographic files at a maintenance level). All are linked to a unique beginner synset, "entity". Noun hierarchies are far deeper than verb hierarchies. Adjectives are not organized into hierarchical trees. Instead, two "central" antonyms such as "hot" and "cold" form binary poles, while 'satellite' synonyms such as "steaming" and "chilly" connect to their respective poles via a "similarity" relations. The adjectives can be visualized in this way as "dumbbells" rather than as "trees". == Psycholinguistic aspects == The initial goal of the WordNet project was to build a lexical database that would be consistent with theories of human semantic memory developed in the late 1960s. Psychological experiments indicated that speakers organized their knowledge of concepts in an economic, hierarchical fashion. Retrieval time required to access conceptual knowledge seemed to be directly related to the number of hierarchies the speaker needed to "traverse" to access the knowledge. Thus, speakers could more quickly verify that canaries can sing because a canary is a songbird, but required slightly more time to verify that canaries can fly (where they had to access the concept "bird" on the superordinate level) and even more time to verify canaries have skin (requiring look-up across multiple levels of hyponymy, up to "animal"). While such psycholinguistic experiments and the underlying theories have been subject to criticism, some of WordNet's organization is consistent with experimental evidence. For example, anomic aphasia selectively affects speakers' ability to produce words from a specific semantic category, a WordNet hierarchy. Antonymous adjectives (WordNet's central adjectives in the dumbbell structure) are found to co-occur far more frequently than chance, a fact that has been found to hold for many languages. == As a lexical ontology == WordNet is sometimes called an ontology, a persistent claim that its creators do not make. The hypernym/hyponym relationships among the noun synsets can be interpreted as specialization relations among conceptual categories. In other words, WordNet can be interpreted and used as a lexical ontology in the computer science sense. However, such an ontology should be corrected before being used, because it contains hundreds of basic semantic inconsistencies; for example there are, (i) common specializations for exclusive categories and (ii) redundancies in the specialization hierarchy. Furthermore, transforming WordNet into a lexical ontology usable for knowledge representation should normally also involve (i) distinguishing the specialization relations into subtypeOf and instanceOf relations, and (ii) associating intuitive unique identifiers to each category. Although such corrections and transformations have been performed and documented as part of the integration of WordNet 1.7 into the cooperatively updatable knowledge base of WebKB-2, most projects claiming to reuse WordNet for knowledge-based applications (typically, knowledge-oriented information retrieval) simply reuse it directly. WordNet has also been converted to a formal specification, by means of a hybrid bottom-up top-down methodology to automatically extract association relations from it and interpret these associations in terms of a set of conceptual relations, formally defined in the DOLCE foundational ontology. In most works that claim to have integrated WordNet into ontologies, the content of WordNet has not simply been corrected when it seemed necessary; instead, it has been heavily reinterpreted and updated whenever suitable. This was the case when, for example, the top-level ontology of WordNet was restructured according to the OntoClean-based approach, or when it was used as a primary source for constructing the lower classes of the SENSUS ontology. == Limitations == The most widely discussed limitation of WordNet (and related resources like ImageNet) is that some of the semantic relations are more suited to concrete concepts than to abstract concepts. For example,
Structural synthesis of programs
Structural synthesis of programs (SSP) is a special form of (automatic) program synthesis that is based on propositional calculus. More precisely, it uses intuitionistic logic for describing the structure of a program in such a detail that the program can be automatically composed from pieces like subroutines or even computer commands. It is assumed that these pieces have been implemented correctly, hence no correctness verification of these pieces is needed. SSP is well suited for automatic composition of services for service-oriented architectures and for synthesis of large simulation programs. == History == Automatic program synthesis began in the artificial intelligence field, with software intended for automatic problem solving. The first program synthesizer was developed by Cordell Green in 1969. At about the same time, mathematicians including R. Constable, Z. Manna, and R. Waldinger explained the possible use of formal logic for automatic program synthesis. Practically applicable program synthesizers appeared considerably later. The idea of structural synthesis of programs was introduced at a conference on algorithms in modern mathematics and computer science organized by Andrey Ershov and Donald Knuth in 1979. The idea originated from G. Pólya’s well-known book on problem solving. The method for devising a plan for solving a problem in SSP was presented as a formal system. The inference rules of the system were restructured and justified in logic by G. Mints and E. Tyugu in 1982. A programming tool PRIZ that uses SSP was developed in the 1980s. A recent Integrated development environment that supports SSP is CoCoViLa — a model-based software development platform for implementing domain specific languages and developing large Java programs. == The logic of SSP == Structural synthesis of programs is a method for composing programs from already implemented components (e.g. from computer commands or software object methods) that can be considered as functions. A specification for synthesis is given in intuitionistic propositional logic by writing axioms about the applicability of functions. An axiom about the applicability of a function f is a logical implication X1 ∧ X2 ∧ ... ∧ Xm → Y1 ∧ Y2 ... Yn, where X1, X2, ... Xm are preconditions and Y1, Y2, ... Yn are postconditions of the application of the function f. In intuitionistic logic, the function f is called a realization of this formula. A precondition can be a proposition stating that input data exists, e.g. Xi may have the meaning “variable xi has received a value”, but it may denote also some other condition, e.g. that resources needed for using the function f are available, etc. A precondition may also be an implication of the same form as the axiom given above; then it is called a subtask. A subtask denotes a function that must be available as an input when the function f is applied. This function itself must be synthesized in the process of SSP. In this case, realization of the axiom is a higher order function, i.e., a function that uses another function as an input. For instance, the formula (state → nextState) ∧ initialState → result can specify a higher order function with two inputs and an output result. The first input is a function that has to be synthesized for computing nextState from state, and the second input is initialState. Higher order functions give generality to the SSP – any control structure needed in a synthesized program can be preprogrammed and used then automatically with a respective specification. In particular, the last axiom presented here is a specification of a complex program – a simulation engine for simulating dynamic systems on models where nextState can be computed from state of the system.
Minimum information standard
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the wider scientific community. Ultimately, they facilitate the transfer of data from journal articles (unstructured data) into databases (structured data) in a form that enables data to be mined across multiple data sets. Minimal information standards are available for a vast variety of experiment types including microarray (MIAME), RNAseq (MINSEQE), metabolomics (MSI) and proteomics (MIAPE). Minimum information standards typically have two parts. Firstly, there is a set of reporting requirements – typically presented as a table or a checklist. Secondly, there is a data format. Information about an experiment needs to be converted into the appropriate data format for it to be submitted to the relevant database. In the case of MIAME, the data format is provided in spreadsheet format (MAGE-TAB). Some of the communities that maintain minimum information standards also provide tools to help experimental researchers to annotate their data. == MI Standards == The individual minimum information standards are brought by the communities of cross-disciplinary specialists focused on the problematic of the specific method used in experimental biology. The standards then provide specifications what information about the experiments (metadata) is crucial and important to be reported together with the resultant data to make it comprehensive. The need for this standardization is largely driven by the development of high-throughput experimental methods that provide tremendous amounts of data. The development of minimum information standards of different methods is since 2008 being harmonized by "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) project. === MIAPPE, Minimum Information About a Plant Phenotyping Experiment === MIAPPE is an open, community driven project to harmonize data from plant phenotyping experiments. MIAPPE comprises both a conceptual checklist of metadata required to adequately describe a plant phenotyping experiment. === MIQE, Minimum Information for Publication of Quantitative Real-Time PCR Experiments === Published in 2009 these guidelines for the basis of requirements by many journals when submitting QPCR data, sadly they are not adhered to enough. === MIAME, gene expression microarray === Minimum Information About a Microarray Experiment (MIAME) describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment and is aimed at facilitating the dissemination of data from microarray experiments. It was published by the FGED Society in 2001 and was the first published minimum information standard for high-throughput experiments in the life sciences. MIAME contains a number of extensions to cover specific biological domains, including MIAME-env, MIAME-nut and MIAME-tox, covering environmental genomics, nutritional genomics and toxogenomics, respectively. === MINI: Minimum Information about a Neuroscience Investigation === ==== MINI: Electrophysiology ==== Electrophysiology is a technology used to study the electrical properties of biological cells and tissues. Electrophysiology typically involves the measurements of voltage change or electric current flow on a wide variety of scales from single ion channel proteins to whole tissues. This document is a single module, as part of the Minimum Information about a Neuroscience investigation (MINI) family of reporting guideline documents, produced by community consultation and continually available for public comment. A MINI module represents the minimum information that should be reported about a dataset to facilitate computational access and analysis to allow a reader to interpret and critically evaluate the processes performed and the conclusions reached, and to support their experimental corroboration. In practice a MINI module comprises a checklist of information that should be provided (for example about the protocols employed) when a data set is described for publication. The full specification of the MINI module can be found here. === MIARE, RNAi experiment === Minimum Information About an RNAi Experiment (MIARE) is a data reporting guideline which describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. === MIACA, cell based assay === Advances in genomics and functional genomics have enabled large-scale analyses of gene and protein function by means of high-throughput cell biological analyses. Thereby, cells in culture can be perturbed in vitro and the induced effects recorded and analyzed. Perturbations can be triggered in several ways, for instance with molecules (siRNAs, expression constructs, small chemical compounds, ligands for receptors, etc.), through environmental stresses (such as temperature shift, serum starvation, oxygen deprivation, etc.), or combinations thereof. The cellular responses to such perturbations are analyzed in order to identify molecular events in the biological processes addressed and understand biological principles. We propose the Minimum Information About a Cellular Assay (MIACA) for reporting a cellular assay, and CA-OM, the modular cellular assay object model, to facilitate exchange of data and accompanying information, and to compare and integrate data that originate from different, albeit complementary approaches, and to elucidate higher order principles. Documents describing MIACA are available and provide further information as well as the checklist of terms that should be reported. === MIAPE, proteomic experiments === The Minimum Information About a Proteomic Experiment documents describe information which should be given along with a proteomic experiment. The parent document describes the processes and principles underpinning the development of a series of domain specific documents which now cover all aspects of a MS-based proteomics workflow. === MIMIx, molecular interactions === This document has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info) and describes the Minimum Information about a Molecular Interaction experiment. === MIAPAR, protein affinity reagents === The Minimum Information About a Protein Affinity Reagent has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info)in conjunction with the HUPO Antibody Initiative and a European consortium of binder producers and seeks to encourage users to improve their description of binding reagents, such as antibodies, used in the process of protein identification. === MIABE, bioactive entities === The Minimum Information About a Bioactive Entity was produced by representatives from both large pharma and academia who are looking to improve the description of usually small molecules which bind to, and potentially modulate the activity of, specific targets in a living organism. This document encompasses drug-like molecules as well as herbicides, pesticides and food additives. It is primarily maintained through the EMBL-EBI Industry program (www.ebi.ac.uk/industry). === MIGS/MIMS, genome/metagenome sequences === This specification is being developed by the Genomic Standards Consortium === MIFlowCyt, flow cytometry === === Minimum Information about a Flow Cytometry Experiment === The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) is a standard related to flow cytometry which establishes criteria to record information on experimental overview, samples, instrumentation and data analysis. It promotes consistent annotation of clinical, biological and technical issues surrounding a flow cytometry experiment. === MINDR, dual gene expression reporters === Requires (1) reporting absolute values of reporter readouts, (2) list of positive and negative controls, and (3) sequences of all reporter constructs. === MISFISHIE, In Situ Hybridization and Immunohistochemistry Experiments === === MIAPA, Phylogenetic Analysis === Criteria for Minimum Information About a Phylogenetic Analysis were described in 2006. === MIRAGE, Glycomics === The MIRAGE project is supported and coordinated by the Beilstein-Institut to establish guidelines for data handling and processing in glycomics research [1] === MIAO, ORF === === MIAMET, METabolomics experiment === === MIAFGE, Functional Genomics Experiment === === MIRIAM, Minimum Information Required in the Annotation of Models === The Minimal Information Required In the Annotation of Models (MIRIAM), is a set of rules for the curation and annotation of quantitative models of biological systems. === MIASE, Minimum Information About a Simulation Experiment =