Linagora is a French open source software editor, founded in June 2000 by Alexandre Zapolsky and Michel-Marie Maudet. Located in France, as well as in Belgium, Canada, Vietnam, the United States and Tunisia, the company employs around 200 people. In 2023, Linagora created the OpenLLM France community, alongside other French Artificial Intelligence companies and organizations. In 2025, the company launched Lucie, an opensource Large Language Model. == History == Linagora was founded on June 28, 2000. Its name is a contraction of the words "Linux" and "Agora". The company was founded by Alexandre Zapolsky and Michel-Marie Maudet. Soon after, the two entrepreneurs were joined by Alexandre Zapolsky's wife and brother, who took on the roles of commercial director and administrative and financial director of the SME. In 2007, the company was selected by the French National Assembly to provide the software for Linux computers, replacing Microsoft Windows. Linagora then claimed the position of the leading French open source software company by revenue. In 2015, French Prime Minister Manuel Valls allocated €10.7 million from the "Investments for the Future" fund for a research program aimed at developing a new generation of open source software platforms based on Linagora's offerings. In September 2016, Linagora launched the social network "La Cerise" for the newspaper L'Humanité. This app offered a service and tool for readers and citizens mobilizing for causes. It aimed to share engagement through petitions, discussions, agendas, and contacts. In October 2016, the company won two public contracts for supporting open source software in forty-two French ministries and other administrative entities. In May 2019, Linagora organized a fundraising event in the presence of the French Secretary of State for Digital Affairs, Cédric O, to celebrate its 19th anniversary. The funds were intended for: Supporting parents of hospitalized Polynesian children in France. Equipping primary school students with digital devices (tablets or PCs). Establishing a digital academy "OpenHackademy" in French Polynesia to train unemployed youth in digital skills and help them find jobs. In December 2022, Linagora acquired a property known as "Maison Rocher" and later "Maison Chocolat," located on the Île Saint-Germain in Issy-les-Moulineaux. Renamed "Villa Good Tech" by Linagora, this award-winning architectural work by Éric Daniel-Lacombe became the company's new headquarters, aiming to provide a space for associative actors and companies to develop technologies that contribute to a better world. In July 2023, Linagora launched OpenLLM France, a community initially comprising around twenty actors focused on generative AI. The goal was to develop a sovereign and open source large language model. This initiative, led by co-founder and CEO Michel-Marie Maudet, had more than four hundred French members by early 2024. and announced its expansion to the European sphere during Fosdem 2024. In February 2024, the CNRS and Linagora signed a framework agreement to strengthen their research collaboration. In January 2025, Linagora released Lucie, an open source and sovereign AI that faced ridicule due to tests on an unfinished, uncensored version designed for scientific and experimental use. The platform divided opinions between those who saw it as a technological achievement and those who criticized it as "French bashing" compared to American and Chinese AIs. == Acquisitions == The company acquired: In July 2007, the SME AliaSource, based in Ramonville-Saint-Agne and led by its founder, Pierre Baudracco. In 2008, the open source web hosting company Netaktiv, a member of the GIE Gitoyen, announced during the 2008 Solutions Linux trade show. In 2012, the Toulouse-based company EBM Websourcing, the publisher of the open-source software Petals Link, and took over its development. In 2016, the digital agency Neoma Interactive, specializing in UX design and digital communication strategy. == Locations == In 2017, the company's headquarters was located in Issy-les-Moulineaux, with branches in Lyon, Toulouse, Marseille, and internationally in Brussels, San Francisco, Montreal, Vietnam, and Tunisia. In 2005, the company attempted to establish a presence in Nantes. In 2024, the headquarters was moved to Issy-les-Moulineaux. == Activity == === Software === Twake Workplace One of Linagora's flagship products is Twake Workplace, which stands out as a 100% open-source solution compared with those of the GAFAMs. Twake Workplace is available as a complete platform or module by module. It includes : Twake Mail, a powerful modern messaging solution based on the JMAP protocol and the James email server from the Apache Foundation, for which Linagora provides technical management; Twake Chat, an instant communications solution for businesses developed using the Matrix protocol and compatible with the French government's chat solution, Tchap; Twake Drive, an easy-to-use collaborative platform for group work using OnlyOffice. ==== OpenPaaS ==== In 2018, the search engine Qwant announced that its email service Qwantmail would be based on the OpenPaaS product. In 2022, Qwant announced the abandonment of its Qwantmail project due to Linagora's collection of personal email addresses and serious security breaches. The site Next (formerly PC INpact) published an article in January 2020 criticizing the "failures and delays" of the Qwantmail project led by Linagora, which led to the CNIL's intervention regarding Qwant and Linagora. ==== LinTO ==== In 2017, Linagora launched its open source voice assistant project named LinTO. This enterprise voice assistant, described as "GAFAM Free," was presented at CES 2018 in Las Vegas. The LinTO voice framework was developed as part of the eponymous research project funded by Bpifrance (Grands Défis du Numérique instrument). === Services === ==== OSSA (Open Source Software Assurance) ==== One of the company's main activities is OSSA. Through OSSA, Linagora provided support for open source software for 42 ministries and other administrative entities in 2012. == Legal issues == === Dispute with BlueMind === In 2012, a legal dispute arose between BlueMind and Linagora. Linagora accused BlueMind of copyright infringement, unfair competition, and breach of a non-compete clause, leading to several legal actions. Linagora sued BlueMind for copyright infringement and unfair competition in the Bordeaux court, which ruled in Linagora's favor for unfair competition and parasitism but rejected the copyright claim. BlueMind was ordered to pay nearly €170,000 to Linagora. Linagora sued former associates Pierre Baudracco and Pierre Carlier in the Paris Commercial Court for breach of a non-compete clause and violation of a warranty of eviction. The court dismissed Linagora's claims and ordered it to pay €20,000 each to Baudracco and Carlier. Linagora appealed, and the Paris Court of Appeal partially overturned the decision, awarding Linagora €480,000. BlueMind sued Linagora for defamation and public insult in the Toulouse Criminal Court. The court ruled against Linagora, but the decision was overturned by the Court of Cassation in January 2024, and the case was remanded for retrial. === Conviction for wrongful termination and harassment === On June 14, 2017, France 3 reported on a decision by the Versailles Court of Appeal, which ruled that Linagora had wrongfully terminated an employee and subjected them to moral harassment. The court ordered Linagora to pay the employee €22,000 for wrongful termination, €11,000 for notice pay, €6,600 for legal severance pay, €3,200 for conservative suspension, and €3,000 for moral harassment.
Oculus Medium
Oculus Medium is a digital sculpting software that works with virtual reality headsets and 6DoF motion controllers. It is used to create and paint digital sculptures. Medium works only on Oculus Rift. It was released on December 5, 2016, following with a major update in 2018 introducing new features and a revamped UI. On December 9, 2019, Oculus Medium was acquired by Adobe and re-named to "Medium by Adobe".
Automated Lip Reading
Automated Lip Reading (ALR) is a software technology developed by speech recognition expert Frank Hubner. A video image of a person talking can be analysed by the software. The shapes made by the lips can be examined and then turned into sounds. The sounds are compared to a dictionary to create matches to the words being spoken. The technology was used successfully to analyse silent home movie footage of Adolf Hitler taken by Eva Braun at their Bavarian retreat Berghof. The video, with words, was included in a documentary titled "Hitler's Private World", Revealed Studios, 2006 Source: New Technology catches Hitler off guard
RIPAC (microprocessor)
RIPAC was a VLSI single-chip microprocessor designed for automatic recognition of the connected speech, one of the first of this use. The project of the microprocessor RIPAC started in 1984. RIPAC was aimed to provide efficient real-time speech recognition services to the italian telephone system provided by SIP. The microprocessor was presented in September 1986 at The Hague (Netherlands) at EUSPICO conference. It was composed of 70.000 transistors and structured as Harvard architecture. The name RIPAC is the acronym for "Riconoscimento del PArlato Connesso", that means "Recognition of the connected speech" in Italian. The microprocessor was designed by the Italian companies CSELT and ELSAG and was produced by SGS: a combination of Hidden Markov Model and Dynamic Time Warping algorithms was used for processing speech signals. It was able to do real-time speech recognition of Italian and many languages with a good affordability. The chip, issued by U.S. Patent No. 4,907,278, worked at first run.
Oversampled binary image sensor
An oversampled binary image sensor is an image sensor with non-linear response capabilities reminiscent of traditional photographic film. Each pixel in the sensor has a binary response, giving only a one-bit quantized measurement of the local light intensity. The response function of the image sensor is non-linear and similar to a logarithmic function, which makes the sensor suitable for high dynamic range imaging. == Working principle == Before the advent of digital image sensors, photography, for the most part of its history, used film to record light information. At the heart of every photographic film are a large number of light-sensitive grains of silver-halide crystals. During exposure, each micron-sized grain has a binary fate: Either it is struck by some incident photons and becomes "exposed", or it is missed by the photon bombardment and remains "unexposed". In the subsequent film development process, exposed grains, due to their altered chemical properties, are converted to silver metal, contributing to opaque spots on the film; unexposed grains are washed away in a chemical bath, leaving behind the transparent regions on the film. Thus, in essence, photographic film is a binary imaging medium, using local densities of opaque silver grains to encode the original light intensity information. Thanks to the small size and large number of these grains, one hardly notices this quantized nature of film when viewing it at a distance, observing only a continuous gray tone. The oversampled binary image sensor is reminiscent of photographic film. Each pixel in the sensor has a binary response, giving only a one-bit quantized measurement of the local light intensity. At the start of the exposure period, all pixels are set to 0. A pixel is then set to 1 if the number of photons reaching it during the exposure is at least equal to a given threshold q. One way to build such binary sensors is to modify standard memory chip technology, where each memory bit cell is designed to be sensitive to visible light. With current CMOS technology, the level of integration of such systems can exceed 109~1010 (i.e., 1 giga to 10 giga) pixels per chip. In this case, the corresponding pixel sizes (around 50~nm ) are far below the diffraction limit of light, and thus the image sensor is oversampling the optical resolution of the light field. Intuitively, one can exploit this spatial redundancy to compensate for the information loss due to one-bit quantizations, as is classic in oversampling delta-sigma converters. Building a binary sensor that emulates the photographic film process was first envisioned by Fossum, who coined the name digital film sensor (now referred to as a quanta image sensor). The original motivation was mainly out of technical necessity. The miniaturization of camera systems calls for the continuous shrinking of pixel sizes. At a certain point, however, the limited full-well capacity (i.e., the maximum photon-electrons a pixel can hold) of small pixels becomes a bottleneck, yielding very low signal-to-noise ratios (SNRs) and poor dynamic ranges. In contrast, a binary sensor whose pixels need to detect only a few photon-electrons around a small threshold q has much less requirement for full-well capacities, allowing pixel sizes to shrink further. == Imaging model == === Lens === Consider a simplified camera model shown in Fig.1. The λ 0 ( x ) {\displaystyle \lambda _{0}(x)} is the incoming light intensity field. By assuming that light intensities remain constant within a short exposure period, the field can be modeled as only a function of the spatial variable x {\displaystyle x} . After passing through the optical system, the original light field λ 0 ( x ) {\displaystyle \lambda _{0}(x)} gets filtered by the lens, which acts like a linear system with a given impulse response. Due to imperfections (e.g., aberrations) in the lens, the impulse response, a.k.a. the point spread function (PSF) of the optical system, cannot be a Dirac delta, thus, imposing a limit on the resolution of the observable light field. However, a more fundamental physical limit is due to light diffraction. As a result, even if the lens is ideal, the PSF is still unavoidably a small blurry spot. In optics, such diffraction-limited spot is often called the Airy disk, whose radius R a {\displaystyle R_{a}} can be computed as R a = 1.22 w f , {\displaystyle R_{a}=1.22\,wf,} where w {\displaystyle w} is the wavelength of the light and f {\displaystyle f} is the F-number of the optical system. Due to the lowpass (smoothing) nature of the PSF, the resulting λ ( x ) {\displaystyle \lambda (x)} has a finite spatial-resolution, i.e., it has a finite number of degrees of freedom per unit space. === Sensor === Fig.2 illustrates the binary sensor model. The s m {\displaystyle s_{m}} denote the exposure values accumulated by the sensor pixels. Depending on the local values of s m {\displaystyle s_{m}} , each pixel (depicted as "buckets" in the figure) collects a different number of photons hitting on its surface. y m {\displaystyle y_{m}} is the number of photons impinging on the surface of the m {\displaystyle m} th pixel during an exposure period. The relation between s m {\displaystyle s_{m}} and the photon count y m {\displaystyle y_{m}} is stochastic. More specifically, y m {\displaystyle y_{m}} can be modeled as realizations of a Poisson random variable, whose intensity parameter is equal to s m {\displaystyle s_{m}} , As a photosensitive device, each pixel in the image sensor converts photons to electrical signals, whose amplitude is proportional to the number of photons impinging on that pixel. In a conventional sensor design, the analog electrical signals are then quantized by an A/D converter into 8 to 14 bits (usually the more bits the better). But in the binary sensor, the quantizer is 1 bit. In Fig.2, b m {\displaystyle b_{m}} is the quantized output of the m {\displaystyle m} th pixel. Since the photon counts y m {\displaystyle y_{m}} are drawn from random variables, so are the binary sensor output b m {\displaystyle b_{m}} . === Spatial and temporal oversampling === If it is allowed to have temporal oversampling, i.e., taking multiple consecutive and independent frames without changing the total exposure time τ {\displaystyle \tau } , the performance of the binary sensor is equivalent to the sensor with same number of spatial oversampling under certain condition. It means that people can make trade off between spatial oversampling and temporal oversampling. This is quite important, since technology usually gives limitation on the size of the pixels and the exposure time. == Advantages over traditional sensors == Due to the limited full-well capacity of conventional image pixel, the pixel will saturate when the light intensity is too strong. This is the reason that the dynamic range of the pixel is low. For the oversampled binary image sensor, the dynamic range is not defined for a single pixel, but a group of pixels, which makes the dynamic range high. == Reconstruction == One of the most important challenges with the use of an oversampled binary image sensor is the reconstruction of the light intensity λ ( x ) {\displaystyle \lambda (x)} from the binary measurement b m {\displaystyle b_{m}} . Maximum likelihood estimation can be used for solving this problem. Fig. 4 shows the results of reconstructing the light intensity from 4096 binary images taken by single photon avalanche diodes (SPADs) camera. A better reconstruction quality with fewer temporal measurements and faster, hardware friendly implementation, can be achieved by more sophisticated algorithms.
Shape context
Shape context is a feature descriptor used in object recognition. Serge Belongie and Jitendra Malik proposed the term in their paper "Matching with Shape Contexts" in 2000. == Theory == The shape context is intended to be a way of describing shapes that allows for measuring shape similarity and the recovering of point correspondences. The basic idea is to pick n points on the contours of a shape. For each point pi on the shape, consider the n − 1 vectors obtained by connecting pi to all other points. The set of all these vectors is a rich description of the shape localized at that point but is far too detailed. The key idea is that the distribution over relative positions is a robust, compact, and highly discriminative descriptor. So, for the point pi, the coarse histogram of the relative coordinates of the remaining n − 1 points, h i ( k ) = # { q ≠ p i : ( q − p i ) ∈ bin ( k ) } {\displaystyle h_{i}(k)=\#\{q\neq p_{i}:(q-p_{i})\in {\mbox{bin}}(k)\}} is defined to be the shape context of p i {\displaystyle p_{i}} . The bins are normally taken to be uniform in log-polar space. The fact that the shape context is a rich and discriminative descriptor can be seen in the figure below, in which the shape contexts of two different versions of the letter "A" are shown. (a) and (b) are the sampled edge points of the two shapes. (c) is the diagram of the log-polar bins used to compute the shape context. (d) is the shape context for the point marked with a circle in (a), (e) is that for the point marked as a diamond in (b), and (f) is that for the triangle. As can be seen, since (d) and (e) are the shape contexts for two closely related points, they are quite similar, while the shape context in (f) is very different. For a feature descriptor to be useful, it needs to have certain invariances. In particular it needs to be invariant to translation, scaling, small perturbations, and, depending on the application, rotation. Translational invariance comes naturally to shape context. Scale invariance is obtained by normalizing all radial distances by the mean distance α {\displaystyle \alpha } between all the point pairs in the shape although the median distance can also be used. Shape contexts are empirically demonstrated to be robust to deformations, noise, and outliers using synthetic point set matching experiments. One can provide complete rotational invariance in shape contexts. One way is to measure angles at each point relative to the direction of the tangent at that point (since the points are chosen on edges). This results in a completely rotationally invariant descriptor. But of course this is not always desired since some local features lose their discriminative power if not measured relative to the same frame. Many applications in fact forbid rotational invariance e.g. distinguishing a "6" from a "9". == Use in shape matching == A complete system that uses shape contexts for shape matching consists of the following steps (which will be covered in more detail in the Details of Implementation section): Randomly select a set of points that lie on the edges of a known shape and another set of points on an unknown shape. Compute the shape context of each point found in step 1. Match each point from the known shape to a point on an unknown shape. To minimize the cost of matching, first choose a transformation (e.g. affine, thin plate spline, etc.) that warps the edges of the known shape to the unknown (essentially aligning the two shapes). Then select the point on the unknown shape that most closely corresponds to each warped point on the known shape. Calculate the "shape distance" between each pair of points on the two shapes. Use a weighted sum of the shape context distance, the image appearance distance, and the bending energy (a measure of how much transformation is required to bring the two shapes into alignment). To identify the unknown shape, use a nearest-neighbor classifier to compare its shape distance to shape distances of known objects. == Details of implementation == === Step 1: Finding a list of points on shape edges === The approach assumes that the shape of an object is essentially captured by a finite subset of the points on the internal or external contours on the object. These can be simply obtained using the Canny edge detector and picking a random set of points from the edges. Note that these points need not and in general do not correspond to key-points such as maxima of curvature or inflection points. It is preferable to sample the shape with roughly uniform spacing, though it is not critical. === Step 2: Computing the shape context === This step is described in detail in the Theory section. === Step 3: Computing the cost matrix === Consider two points p and q that have normalized K-bin histograms (i.e. shape contexts) g(k) and h(k). As shape contexts are distributions represented as histograms, it is natural to use the χ2 test statistic as the "shape context cost" of matching the two points: C S = 1 2 ∑ k = 1 K [ g ( k ) − h ( k ) ] 2 g ( k ) + h ( k ) {\displaystyle C_{S}={\frac {1}{2}}\sum _{k=1}^{K}{\frac {[g(k)-h(k)]^{2}}{g(k)+h(k)}}} The values of this range from 0 to 1. In addition to the shape context cost, an extra cost based on the appearance can be added. For instance, it could be a measure of tangent angle dissimilarity (particularly useful in digit recognition): C A = 1 2 ‖ ( cos ( θ 1 ) sin ( θ 1 ) ) − ( cos ( θ 2 ) sin ( θ 2 ) ) ‖ {\displaystyle C_{A}={\frac {1}{2}}{\begin{Vmatrix}{\dbinom {\cos(\theta _{1})}{\sin(\theta _{1})}}-{\dbinom {\cos(\theta _{2})}{\sin(\theta _{2})}}\end{Vmatrix}}} This is half the length of the chord in unit circle between the unit vectors with angles θ 1 {\displaystyle \theta _{1}} and θ 2 {\displaystyle \theta _{2}} . Its values also range from 0 to 1. Now the total cost of matching the two points could be a weighted-sum of the two costs: C = ( 1 − β ) C S + β C A {\displaystyle C=(1-\beta )C_{S}+\beta C_{A}\!\,} Now for each point pi on the first shape and a point qj on the second shape, calculate the cost as described and call it Ci,j. This is the cost matrix. === Step 4: Finding the matching that minimizes total cost === Now, a one-to-one matching π ( i ) {\displaystyle \pi (i)} that matches each point pi on shape 1 and qj on shape 2 that minimizes the total cost of matching, H ( π ) = ∑ i C ( p i , q π ( i ) ) {\displaystyle H(\pi )=\sum _{i}C\left(p_{i},q_{\pi (i)}\right)} is needed. This can be done in O ( N 3 ) {\displaystyle O(N^{3})} time using the Hungarian method, although there are more efficient algorithms. To have robust handling of outliers, one can add "dummy" nodes that have a constant but reasonably large cost of matching to the cost matrix. This would cause the matching algorithm to match outliers to a "dummy" if there is no real match. === Step 5: Modeling transformation === Given the set of correspondences between a finite set of points on the two shapes, a transformation T : R 2 → R 2 {\displaystyle T:\mathbb {R} ^{2}\to \mathbb {R} ^{2}} can be estimated to map any point from one shape to the other. There are several choices for this transformation, described below. ==== Affine ==== The affine model is a standard choice: T ( p ) = A p + o {\displaystyle T(p)=Ap+o\!} . The least squares solution for the matrix A {\displaystyle A} and the translational offset vector o is obtained by: o = 1 n ∑ i = 1 n ( p i − q π ( i ) ) , A = ( Q + P ) t {\displaystyle o={\frac {1}{n}}\sum _{i=1}^{n}\left(p_{i}-q_{\pi (i)}\right),A=(Q^{+}P)^{t}} Where P = ( 1 p 11 p 12 ⋮ ⋮ ⋮ 1 p n 1 p n 2 ) {\displaystyle P={\begin{pmatrix}1&p_{11}&p_{12}\\\vdots &\vdots &\vdots \\1&p_{n1}&p_{n2}\end{pmatrix}}} with a similar expression for Q {\displaystyle Q\!} . Q + {\displaystyle Q^{+}\!} is the pseudoinverse of Q {\displaystyle Q\!} . ==== Thin plate spline ==== The thin plate spline (TPS) model is the most widely used model for transformations when working with shape contexts. A 2D transformation can be separated into two TPS function to model a coordinate transform: T ( x , y ) = ( f x ( x , y ) , f y ( x , y ) ) {\displaystyle T(x,y)=\left(f_{x}(x,y),f_{y}(x,y)\right)} where each of the ƒx and ƒy have the form: f ( x , y ) = a 1 + a x x + a y y + ∑ i = 1 n ω i U ( ‖ ( x i , y i ) − ( x , y ) ‖ ) , {\displaystyle f(x,y)=a_{1}+a_{x}x+a_{y}y+\sum _{i=1}^{n}\omega _{i}U\left({\begin{Vmatrix}(x_{i},y_{i})-(x,y)\end{Vmatrix}}\right),} and the kernel function U ( r ) {\displaystyle U(r)\!} is defined by U ( r ) = r 2 log r 2 {\displaystyle U(r)=r^{2}\log r^{2}\!} . The exact details of how to solve for the parameters can be found elsewhere but it essentially involves solving a linear system of equations. The bending energy (a measure of how much transformation is needed to align the points) will also be easily obtained. ==== Regularized TPS ==== The TPS formulation above has exact matching requirement for the pairs of points on the two shapes. For noisy data, it is best to
Amira (software)
Amira (ah-MEER-ah) is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo. == Overview == Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. It is used by researchers and engineers in academia and industry. It is a tool for processing, analysis and visualization of data from various modalities; e.g. micro-CT, PET, Ultrasound. It is used in many fields, such as microscopy in biology and materials science, molecular biology, quantum physics, astrophysics, computational fluid dynamics (CFD), finite element modeling (FEM), non-destructive testing (NDT), and many more. One of the key features, besides data visualization, is Amira's set of tools for image segmentation and geometry reconstruction. This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis, density analysis, shape analysis, or the generation of 3D computer models for visualization, numerical simulations, or rapid prototyping or 3D printing. Other key Amira features are multi-planar and volume visualization, image registration, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data, skeletonization, spatial graph analysis, and stereoscopic rendering of 3D data over multiple displays and immersive virtual reality environments, including CAVEs. As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge. == History == === 1993–1998: Research software === Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department's mission is to help solve computationally and scientifically challenging tasks in medicine, biology, engineering and materials science. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products' interactivity, flexibility, and ease-of-use for non-computer scientists. Therefore, the development of a new software system was started in a research project within a medically oriented, multi-disciplinary collaborative research center. Based on experiences that Tobias Höllerer had gained in late 1993 with the new graphics library IRIS Inventor, it was decided to utilize that library. The development of the medical planning system was performed by Detlev Stalling, who later became the chief software architect of Amira. The new software was called "HyperPlan", highlighting its initial target application – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. The software was based on libraries such as OpenGL (originally IRIS GL), Open Inventor (originally IRIS Inventor), and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit. The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in medical image computing, medical visualization, neurobiology, confocal microscopy, flow visualization, molecular analytics and computational astrophysics. === 1998–today: Commercially supported product === The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB's primary mission was algorithmic research. Therefore, the spin-off company Indeed – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff. In Feb 1998 the HyperPlan software was given the new, application-neutral name "Amira". This name is not an acronym, but was chosen for being pronounceable in different languages and providing a suitable connotation, namely "to look at" or "to wonder at", from the Latin verb "admirare" (to admire), which reflects a basic situation in data visualization. A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths. Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years. In 2003 both Indeed – Visual Concepts GmbH, as well as TGS, Inc. were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury's newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences. In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. This brought the two software sisters Amira and Avizo back into one hand. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. In 2016 FEI has been bought by Thermo Fisher Scientific and became part of its Materials & Structural Analysis division in early 2017. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. In the meantime, the number of scientific articles using the Amira / Avizo software, is in the order of 10 thousands. == Amira options == === Microscopy option === Specific readers for microscopy data Image deconvolution Exploration of 3D imagery obtained from virtually any microscope Extraction and editing of filament networks from microscopy images === DICOM reader === Import of clinical and preclinical data in DICOM format === Mesh option === Generation of 3D finite element (FE) meshes from segmented image data Support for many state-of-the-art FE solver formats High-quality visualization of simulation mesh-based results, using scalar, vector, and tensor field display modules === Skeletonization option === Reconstruction and analysis of neural and vascular networks Visualization of skeletonized networks Length and diameter quantification of network segments Ordering of segments in a tree graph Skeletonization of very large image stacks === Molecular option === Advanced tools for the visualization of molecule models Hardware-accelerated volume rendering Powerful molecule editor Specific tools for complex molecular visualization === Developer option === Creation of new custom components for visualizing or data processing Implementation of new file readers or writers C++ programming language Development wizard for getting started quickly === Neuro option === Medical image analysis for DTI and brain perfusion Fiber tracking supporting several stream-line based algorithms Fiber separation into fiber bundles based on user defined source and destination regions Computation of tensor fields, diffusion weighted maps Eigenvalue decomposition of tensor fields Computation of mean transit time, cerebral blood flow, and cerebral blood volume === VR option === Visualization of data on large tiled displays