Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, making interpretation difficult. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a three-dimensional reconstruction of the particle. Using cryo-electron microscopy it has become possible to generate reconstructions with sub-nanometer, near-atomic resolution resolution first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well. == Techniques == Single particle analysis can be done on both negatively stained and vitreous ice-embedded transmission electron cryomicroscopy (CryoTEM) samples. Single particle analysis methods are, in general, reliant on the sample being homogeneous, although techniques for dealing with conformational heterogeneity are being developed. Images (micrographs) are taken with an electron microscope using charged-coupled device (CCD) detectors coupled to a phosphorescent layer (in the past, they were instead collected on film and digitized using high-quality scanners). The image processing is carried out using specialized software programs, often run on multi-processor computer clusters. Depending on the sample or the desired results, various steps of two- or three-dimensional processing can be done. === Alignment and classification === Biological samples, and especially samples embedded in thin vitreous ice, are highly radiation sensitive, thus only low electron doses can be used to image the sample. This low dose, as well as variations in the metal stain used (if used) means images have high noise relative to the signal given by the particle being observed. By aligning several similar images to each other so they are in register and then averaging them, an image with higher signal-to-noise ratio can be obtained. As the noise is mostly randomly distributed and the underlying image features constant, by averaging the intensity of each pixel over several images only the constant features are reinforced. Typically, the optimal alignment (a translation and an in-plane rotation) to map one image onto another is calculated by cross-correlation. However, a micrograph often contains particles in multiple different orientations and/or conformations, and so to get more representative image averages, a method is required to group similar particle images together into multiple sets. This is normally carried out using one of several data analysis and image classification algorithms, such as multi-variate statistical analysis and hierarchical ascendant classification, or k-means clustering. Often data sets of tens of thousands of particle images are used, and to reach an optimal solution an iterative procedure of alignment and classification is used, whereby strong image averages produced by classification are used as reference images for a subsequent alignment of the whole data set. === Image filtering === Image filtering (band-pass filtering) is often used to reduce the influence of high and/or low spatial frequency information in the images, which can affect the results of the alignment and classification procedures. This is particularly useful in negative stain images. The algorithms make use of fast Fourier transforms (FFT), often employing Gaussian shaped soft-edged masks in reciprocal space to suppress certain frequency ranges. High-pass filters remove low spatial frequencies (such as ramp or gradient effects), leaving the higher frequencies intact. Low-pass filters remove high spatial frequency features and have a blurring effect on fine details. === Contrast transfer function === Due to the nature of image formation in the electron microscope, bright-field TEM images are obtained using significant underfocus. This, along with features inherent in the microscope's lens system, creates blurring of the collected images visible as a point spread function. The combined effects of the imaging conditions are known as the contrast transfer function (CTF), and can be approximated mathematically as a function in reciprocal space. Specialized image processing techniques such as phase flipping and amplitude correction / Wiener filtering can (at least partially) correct for the CTF, and allow high resolution reconstructions. === Three-dimensional reconstruction === Transmission electron microscopy images are projections of the object showing the distribution of density through the object, similar to medical X-rays. By making use of the projection-slice theorem a three-dimensional reconstruction of the object can be generated by combining many images (2D projections) of the object taken from a range of viewing angles. Proteins in vitreous ice ideally adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic reconstruction if a large number of particle images are used. This contrasts with electron tomography, where the viewing angles are limited due to the geometry of the sample/imaging set up, giving an anisotropic reconstruction. Filtered back projection is a commonly used method of generating 3D reconstructions in single particle analysis, although many alternative algorithms exist. Before a reconstruction can be made, the orientation of the object in each image needs to be estimated. Several methods have been developed to work out the relative Euler angles of each image. Some are based on common lines (common 1D projections and sinograms), others use iterative projection matching algorithms. The latter works by beginning with a simple, low resolution 3D starting model and compares the experimental images to projections of the model and creates a new 3D to bootstrap towards a solution. Methods are also available for making 3D reconstructions of helical samples (such as tobacco mosaic virus), taking advantage of the inherent helical symmetry. Both real space methods (treating sections of the helix as single particles) and reciprocal space methods (using diffraction patterns) can be used for these samples. === Tilt methods === The specimen stage of the microscope can be tilted (typically along a single axis), allowing the single particle technique known as random conical tilt. An area of the specimen is imaged at both zero and at high angle (~60-70 degrees) tilts, or in the case of the related method of orthogonal tilt reconstruction, +45 and −45 degrees. Pairs of particles corresponding to the same object at two different tilts (tilt pairs) are selected, and by following the parameters used in subsequent alignment and classification steps a three-dimensional reconstruction can be generated relatively easily. This is because the viewing angle (defined as three Euler angles) of each particle is known from the tilt geometry. 3D reconstructions from random conical tilt suffer from missing information resulting from a restricted range of orientations. Known as the missing cone (due to the shape in reciprocal space), this causes distortions in the 3D maps. However, the missing cone problem can often be overcome by combining several tilt reconstructions. Tilt methods are best suited to negatively stained samples, and can be used for particles that adsorb to the carbon support film in preferred orientations. The phenomenon known as charging or beam-induced movement makes collecting high-tilt images of samples in vitreous ice challenging. === Map visualization and fitting === Various software programs are available that allow viewing the 3D maps. These often enable the user to manually dock in protein coordinates (structures from X-ray crystallography, NMR, or a computational model such as one found in the AlphaFold Protein Structure Database) of subunits into the electron density. Several programs can also fit subunits computationally; as of the 2020s using these programs tend to produce better accuracy than manual docking because they can perform labor-intensive tasks such as: The scale of SPA-derived maps depends on knowing the pixel size (angstorms per pixel), which is not always accurate. Programs can automatically correct for this difference by using coordinate data or by using knowledge of chemical bonds. Many proteins are made up of several roughly rigid protein domains linked by flexible parts. Pre-existing coordinate data, whether experimental or computational, may not exactly match the inter-domain positioning of the cyro-EM map. Modern programs can automatically "chop" pre-existing coordinate data into individual domains and fit them in individually. For higher-resolution structures, it is pos
Caffe (software)
Caffe (Convolutional Architecture for Fast Feature Embedding) is a deep learning framework, originally developed at University of California, Berkeley. It is open source, under a BSD license. It is written in C++, with a Python interface. == History == Yangqing Jia created the Caffe project during his PhD at UC Berkeley, while working the lab of Trevor Darrell. The first version, called "DeCAF", made its first appearance in Spring 2013 when it was used for the ILSVRC challenge (later called ImageNet). The library was named Caffe and released to the public in December 2013. It reached end-of-support in 2018. It is hosted on GitHub. == Features == Caffe supports many different types of deep learning architectures geared towards image classification and image segmentation. It supports CNN, RCNN, LSTM and fully-connected neural network designs. Caffe supports GPU- and CPU-based acceleration computational kernel libraries such as Nvidia cuDNN and Intel MKL. == Applications == Caffe is being used in academic research projects, startup prototypes, and even large-scale industrial applications in vision, speech, and multimedia. Yahoo! has also integrated Caffe with Apache Spark to create CaffeOnSpark, a distributed deep learning framework. == Caffe2 == In April 2017, Facebook announced Caffe2, which included new features such as recurrent neural network (RNN). At the end of March 2018, Caffe2 was merged into PyTorch.
Dave's Redistricting
Dave's Redistricting App (DRA) is an online web app originally created by Dave Bradlee that allows anyone to simulate redistricting a U.S. state's congressional and legislative districts. == Purpose == According to Bradlee, the software was designed to "put power in people's hands," and so that they "can see how the process works, so it's a little less mysterious than it was 10 years ago." Bradlee has noticed that many citizens are taking this process seriously and using his app to create legitimate redistricting maps that could be put in place. Some websites have called Bradlee the pioneer and cause of the rise of do-it-yourself redistricting. States such as Montana in 2021 allowed the general population to use it to submit redistricting proposals following the 2020 United States Census. Dave's Redistricting has frequently been mentioned as a resource that can be used to combat gerrymandering, given that the public has free access to it. Political science firms such as FiveThirtyEight have used the website to draw examples of gerrymandered districts, including on their famous Atlas of Redistricting. Dave Bradlee built the first generation of DRA. DRA 2020 is built by a small team of volunteers—Dave Bradlee, Terry Crowley, Alec Ramsay, and David Rinn—all with a shared passion for technology & democracy and all Microsoft veterans. Their mission is to empower civic organizations and citizen activists to advocate for fair congressional and legislative districts and increased transparency in the redistricting process. == Functions == Users can redraw the congressional and state legislative districts for all 50 states, the District of Columbia, and Puerto Rico using a variety of census and election datasets including Cook PVI. Maps can be optimized for different criteria. DRA 2020 added several major features to the first generation app: Sharing & collaborative editing of maps, like Google Docs Multiple statewide elections for all 50 states including the ability to import your own data Comprehensive analytics for evaluating and comparing maps Custom overlays, and Block-level editing DRA remains free to use. == Versions == 2.2: This uses Bing Maps, an outdated software that projects the districts of a single state onto a map of the United States. 2.5: After Bing Maps announced that it would no longer be updating for the foreseen future, the U.S. Map feature was removed. DRA 2020: At the end of 2018, a beta version of 2020 was released. This version that did not require Microsoft Silverlight and could be used in any web browser. DRA 2020 has been under continuous development since and is built using React (JavaScript library), Mapbox, OpenStreetMap, TypeScript, Node.js, Amazon Web Services, as well as many open source components, tools, and icons.
Teaspiller
Teaspiller was a US-based web application for customers to find accountants and hire them to do their taxes and accounting online. In 2013 the company was acquired by Intuit, Inc and added to its TurboTax product line. The Teaspiller employees and code were all acquired and the product was renamed as "TurboTax CPA select". It enabled accountants to work remotely with clients (share files, send secure messages, schedule appointments), as well as find new clients looking for their specific skills through a complex search algorithm. This was done through extended profiles containing licensing information, professional histories, user ratings, peer endorsements, association memberships, and practice areas. The service had been called an H&R Block killer by Business Insider as it helped customers find accountants to prepare tax returns online. As of 2011 it had 20,000 US accountants listed on the site. The application was built using the Django framework. == History == Teaspiller was built by Vemdara, LLC, a web company based in New York and founded in 2009 by Amit Vemuri (a former VP at Travelocity). The web application was launched in 2010. In 2013 the company was acquired by Intuit as part of their TurboTax product line and renamed as "TurboTax CPA select".
ShowDocument
ShowDocument is an online web application that allows multiple users to conduct web meetings, upload, share and review documents from remote locations. The service was developed by the HBR Labs company, established in 2007. == Features == Users can collaborate on and review documents in real time, with annotations and text being visible to all users and accessible for co-editing. The idea of every user being able to annotate can cause conflicts within the sessions, and so main navigation options are under the "presenter"'s control - which can be given to a different user as well. An earlier version of the application, by contrast, had allowed all users to navigate and edit at once, causing the system to drop all incomplete edits. It is possible to draw and write on a virtual whiteboard, and to stream a YouTube video to a group in full synchronization. A feature also exists for co-browsing of Google Maps. Entering an open session in the application can be done with a given code number, or by receiving a link through an Email message. Different file formats can be uploaded and saved either online or offline, such as PDF. A PDF file's text cannot be edited - text is edited through the separate text editor. Although the platform contains a text chat, it is not intended to replace instant messaging software, as there are no extensive messaging features. The application has a paid and free version, with the free version having a few limitations: audio and video options are disabled, number of participants is limited and sessions are time-limited. == Development == ShowDocument was first developed in 2007. On September 8, 2009, HBR labs released a new update which included features such as secure online document storage and mobile device support.
MeeMix
MeeMix Ltd is a company specializing in personalizing media-related content recommendations, discovery and advertising for the telecommunication industry, founded in 2006. On January 1, 2008, MeeMix launched meemix.com, a public personalized internet radio serving as an online testbed for the development of music taste-prediction technologies. Subsequently, MeeMix released in 2009 a line of Business-to-business commercial services intended to personalize media recommendations, discovery and advertising. MeeMix hybrid taste-prediction technology relies on integrating machine learning algorithms, digital signal processing, behavior analysis, metadata analysis and collaborative filtering, and is provided via API web service. In August 2009, MeeMix was announced as Innovator Nominee in the GSM Association’s Mobile Innovation Grand Prix worldwide contest. As of 2013, MeeMix no longer features internet radios on meemix.com. On Sep 28, 2014, meemix.com went offline.
Tweak programming environment
Tweak is a graphical user interface (GUI) layer written by Andreas Raab for the Squeak development environment, which in turn is an integrated development environment based on the Smalltalk-80 computer programming language. Tweak is an alternative to an earlier graphic user interface layer called Morphic. Development began in 2001. Applications that use the Tweak software include Sophie (version 1), a multimedia and e-book authoring system, and a family of virtual world systems: Open Cobalt, Teleplace, OpenQwaq, 3d ICC's Immersive Terf and the Croquet Project. == Influences == An experimental version of Etoys, a programming environment for children, used Tweak instead of Morphic. Etoys was a major influence on a similar Squeak-based programming environment known as Scratch.