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CellProfiler
CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline; the pipeline is then used to identify and measure biological objects and features in images, particularly those obtained through fluorescence microscopy. Distributions are available for Microsoft Windows, macOS, and Linux. The source code for CellProfiler is freely available. CellProfiler is developed by the Broad Institute's Imaging Platform. Features CellProfiler can read and analyze most common microscopy image formats. Biologists typically use CellProfiler to identify objects of interest (e.g. cells, colonies, ''C. elegans'' worms) and then measure their properties of interest. Specialized modules for illumination correction may be ap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ilastik
ilastik is a user-friendly free open source software for image classification and segmentation. No previous experience in image processing is required to run the software. Features ilastik allows user to annotate an arbitrary number of classes in images with a mouse interface. Using these user annotations and the generic (nonlinear) image features, the user can train a random forest classifier. ilastik has a CellProfiler module to use ilastik classifiers to process images within a CellProfiler framework. History ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg. Application * The Interactive Learning and Segmentation Toolkit * Carving * Cell classification and neuron classification * Synapse detection * Cell tracking Resources ilastik project is hosted on GitHub GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ImageJ
ImageJ is a Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation (LOCI, University of Wisconsin). Its first version, ImageJ 1.x, is developed in the public domain, while ImageJ2 and the related projects SciJava, ImgLib2, and SCIFIO are licensed with a permissive BSD-2 license. ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging to radiological image processing, multiple imaging system data comparisons to automated hematology systems. ImageJ's plugin architecture and built-in development environment has made it a popular platform for teaching image processing. ImageJ can be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anne E
Anne, alternatively spelled Ann, is a form of the Latin female given name Anna. This in turn is a representation of the Hebrew Hannah, which means 'favour' or 'grace'. Related names include Annie. Anne is sometimes used as a male name in the Netherlands, particularly in the Frisian speaking part (for example, author Anne de Vries). In this incarnation, it is related to Germanic arn-names and means 'eagle'.See entry on "Anne" in th''Behind the Name'' databaseand th"Anne"an"Ane"entries (in Dutch) in the Nederlandse Voornamenbank (Dutch First Names Database) of the Meertens Instituut (23 October 2018). It has also been used for males in France ( Anne de Montmorency) and Scotland (Lord Anne Hamilton). Anne is a common name and the following lists represent a small selection. For a comprehensive list, see instead: . As a feminine name Anne * Saint Anne, Mother of the Virgin Mary * Anne, Queen of Great Britain (1665–1714), Queen of England, Scotland, and Ireland (1702–07) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Segmentation (image Processing)
In digital image processing and computer vision, image segmentation is the process of partitioning a digital image into multiple image segments, also known as image regions or image objects ( sets of pixels). The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze. Linda G. Shapiro and George C. Stockman (2001): “Computer Vision”, pp 279–325, New Jersey, Prentice-Hall, Image segmentation is typically used to locate objects and boundaries (lines, curves, etc.) in images. More precisely, image segmentation is the process of assigning a label to every pixel in an image such that pixels with the same label share certain characteristics. The result of image segmentation is a set of segments that collectively cover the entire image, or a set of contours extracted from the image (see edge detection). Each of the pixels in a region are similar with respect to some characteristic or computed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Whitehead Institute For Biomedical Research
Whitehead Institute for Biomedical Research is a non-profit research institute located in Cambridge, Massachusetts, United States that is dedicated to improving human health through basic biomedical research. It was founded as a fiscally independent entity from the Massachusetts Institute of Technology (MIT), where its 18 members all hold faculty appointments in the MIT Department of Biology or the MIT Department of Bioengineering. Two members (Rudolf Jaenisch, 2010, and Robert Weinberg, 1997) are National Medal of Science recipients; ten have been elected to the National Academy of Sciences; and four have been elected to the National Academy of Medicine; six are Howard Hughes Medical Institute Investigators. In September 2019, Ruth Lehmann was announced as the new director of the Whitehead Institute for Biomedical Research, commencing July 2020 and succeeding David Page. History Whitehead Institute was founded in 1982 by industrialist and philanthropist Edwin C. “Jack ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Time-lapse Microscopy
Time-lapse microscopy is time-lapse photography applied to microscopy. Microscope image sequences are recorded and then viewed at a greater speed to give an accelerated view of the microscopic process. Before the introduction of the video tape recorder in the 1960s, time-lapse microscopy recordings were made on photographic film. During this period, time-lapse microscopy was referred to as microcinematography. With the increasing use of video recorders, the term time-lapse video microscopy was gradually adopted. Today, the term video is increasingly dropped, reflecting that a digital still camera is used to record the individual image frames, instead of a video recorder. Applications Time-lapse microscopy can be used to observe any microscopic object over time. However, its main use is within cell biology to observe artificially cultured cells. Depending on the cell culture, different microscopy techniques can be applied to enhance characteristics of the cells as most cells ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SciPy
SciPy (pronounced "sigh pie") is a free and open-source Python library used for scientific computing and technical computing. SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and engineering. SciPy is also a family of conferences for users and developers of these tools: SciPy (in the United States), EuroSciPy (in Europe) and SciPy.in (in India). Enthought originated the SciPy conference in the United States and continues to sponsor many of the international conferences as well as host the SciPy website. The SciPy library is currently distributed under the BSD license, and its development is sponsored and supported by an open community of developers. It is also supported by NumFOCUS, a community foundation for supporting reproducible and accessible science. Components The SciPy package is at the core of Python's scientific computing capabilit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SQLite
SQLite (, ) is a database engine written in the C programming language. It is not a standalone app; rather, it is a library that software developers embed in their apps. As such, it belongs to the family of embedded databases. It is the most widely deployed database engine, as it is used by several of the top web browsers, operating systems, mobile phones, and other embedded systems. Many programming languages have bindings to the SQLite library. It generally follows PostgreSQL syntax, but does not enforce type checking by default. This means that one can, for example, insert a string into a column defined as an integer. History D. Richard Hipp designed SQLite in the spring of 2000 while working for General Dynamics on contract with the United States Navy. Hipp was designing software used for a damage-control system aboard guided-missile destroyers, which originally used HP-UX with an IBM Informix database back-end. SQLite began as a Tcl extension. In August 2000, versio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MySQL
MySQL () is an open-source relational database management system (RDBMS). Its name is a combination of "My", the name of co-founder Michael Widenius's daughter My, and "SQL", the acronym for Structured Query Language. A relational database organizes data into one or more data tables in which data may be related to each other; these relations help structure the data. SQL is a language programmers use to create, modify and extract data from the relational database, as well as control user access to the database. In addition to relational databases and SQL, an RDBMS like MySQL works with an operating system to implement a relational database in a computer's storage system, manages users, allows for network access and facilitates testing database integrity and creation of backups. MySQL is free and open-source software under the terms of the GNU General Public License, and is also available under a variety of proprietary licenses. MySQL was owned and sponsored by the Swedish com ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Spreadsheet
A spreadsheet is a computer application for computation, organization, analysis and storage of data in tabular form. Spreadsheets were developed as computerized analogs of paper accounting worksheets. The program operates on data entered in cells of a table. Each cell may contain either numeric or text data, or the results of formulas that automatically calculate and display a value based on the contents of other cells. The term ''spreadsheet'' may also refer to one such electronic document. Spreadsheet users can adjust any stored value and observe the effects on calculated values. This makes the spreadsheet useful for "what-if" analysis since many cases can be rapidly investigated without manual recalculation. Modern spreadsheet software can have multiple interacting sheets and can display data either as text and numerals or in graphical form. Besides performing basic arithmetic and mathematical functions, modern spreadsheets provide built-in functions for common financial a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comma-separated Values
A comma-separated values (CSV) file is a delimited text file that uses a comma to separate values. Each line of the file is a data record. Each record consists of one or more fields, separated by commas. The use of the comma as a field separator is the source of the name for this file format. A CSV file typically stores tabular data (numbers and text) in plain text, in which case each line will have the same number of fields. The CSV file format is not fully standardized. Separating fields with commas is the foundation, but commas in the data or embedded line breaks have to be handled specially. Some implementations disallow such content while others surround the field with quotation marks, which yet again creates the need for escaping if quotation marks are present in the data. The term "CSV" also denotes several closely-related delimiter-separated formats that use other field delimiters such as semicolons. These include tab-separated values and space-separated values. A d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
