mainpages:links2011
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| + | ====== Links ====== | ||
| + | Links revised on Mar.15, 2012 | ||
| + | |||
| + | [[http:// | ||
| + | [[http:// | ||
| + | [[http:// | ||
| + | |||
| + | ===== Learning ===== | ||
| + | |||
| + | **Textbooks (web-accessible)** | ||
| + | |||
| + | * [[http:// | ||
| + | * All chapters downloadable | ||
| + | * [[http:// | ||
| + | * 2nd edition. Better updates are available in thr 3rd Ed (then not free, or library). | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * A list of free CV books available on the web | ||
| + | * [[http:// | ||
| + | * A list of free SP books available on the web | ||
| + | |||
| + | **Tutorials** | ||
| + | |||
| + | * CMCI TextBook I: [[https:// | ||
| + | * PDF. Learning Basics using ImageJ. | ||
| + | * CMCI Textbook II: [[https:// | ||
| + | * PDF. IJ Macro from very beginning and also primer for Javascript. | ||
| + | * [[http:// | ||
| + | * short tutorial @ National Instruments | ||
| + | * [[http:// | ||
| + | * detailed hyper texts | ||
| + | * [[http:// | ||
| + | * Detailed in Microscopy systems | ||
| + | * [[http:// | ||
| + | * for Remote Sensing, but the principle is same. | ||
| + | * [[http:// | ||
| + | * "" | ||
| + | * [[http:// | ||
| + | * Practical lessons for analysis of biolgical data | ||
| + | * [[http:// | ||
| + | * processing tutorial for Photoshop | ||
| + | * [[http:// | ||
| + | * for treating results | ||
| + | * [[http:// | ||
| + | * for 3D Graphic Presentations | ||
| + | |||
| + | ** Tutorials: Scripting ** | ||
| + | |||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Excellent Fiji+Jython tutorial by Albert Cardona. | ||
| + | * [[http:// | ||
| + | |||
| + | * Python Basics | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Python Image Processing: importing image, plotting image and some basics. | ||
| + | |||
| + | |||
| + | ===== Software ===== | ||
| + | |||
| + | All software, except those indicated, are freely available. \\ | ||
| + | **PU** stands for "Power Users", | ||
| + | |||
| + | ==== General ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * **PU** Kota Miura, Christian Tischer | ||
| + | * ImageJ Distributions, | ||
| + | * [[http:// | ||
| + | * Plugin-bundled distribution of ImageJ. "Fiji is Just ImageJ", | ||
| + | * **PU**: Kota Miura, Christian Tischer | ||
| + | * [[http:// | ||
| + | * ImageJ bundled with R. Eclipse like interface. | ||
| + | * [[http:// | ||
| + | * Full integration of ImageJ + Microsopy hardware control. " | ||
| + | * **PU**: Kakosenen lab, Nedelec lab | ||
| + | * [[http:// | ||
| + | * Next generation ImageJ. | ||
| + | * [[http:// | ||
| + | * ImageJ Macro could be used in the pipeline. | ||
| + | * **PU**: Christian Tischer | ||
| + | * [[http:// | ||
| + | * **PU**: Sebastian Streichan, Alex De Marco, Wanqing Xiang, Nedelec lab | ||
| + | * commercial. | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Commercial. | ||
| + | * **PU**: Christian Conrad, Ciaran Behan | ||
| + | * [[http:// | ||
| + | * Commercial. | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Tutorial: see [[http:// | ||
| + | * **PU** Greg Pau, Andrea Picco, Joe Barry | ||
| + | * [[http:// | ||
| + | * Downloadable on inquiry. | ||
| + | * [[http:// | ||
| + | * " | ||
| + | * CellAnalyzer is GUI interface based on CellCognition framework, which is based on Vigra and Machine Learning libraries. Offering a cell image analysis tool combining segmentation and tracking. Multi-channel machine learning. GUI is written in python, and the base framework in C++. | ||
| + | * [[https:// | ||
| + | ==== Segmentation ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * Machine-learning, | ||
| + | * [[http:// | ||
| + | * Machine-learning, | ||
| + | * [[http:// | ||
| + | * Machine-learning, | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Fast Marching and active contour. | ||
| + | * [[http:// | ||
| + | |||
| + | ==== Object Tracking ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * 2D and 3D tracking software. Originally developed for Fluorescence Speckle Microscopy. | ||
| + | * Commercial | ||
| + | * [[http:// | ||
| + | * 2D cell tracking. "We propose a novel edge-based method for sensitive tracking of cells, and propose a scaffold of methods that achieves refined tracking results even under large displacements or deformations of the cells. The proposed methods along with other general purpose image enhancement methods are implemented in CellTrack, a self-contained, | ||
| + | * [[http:// | ||
| + | * "a free software environment for image browsing, processing and cell tracking", | ||
| + | * [[http:// | ||
| + | * "… a manual image analyzing program, written by Gabor Ivancsy. The original purpose of this software was to follow cell and axon movements in image sequences." | ||
| + | * [[http:// | ||
| + | * 2D cell migration tracking and intensity measurement done at the same time. | ||
| + | * [[http:// | ||
| + | * MatLab m-file. see also [[http:// | ||
| + | * [[http:// | ||
| + | * ImageJ plugin for particle tracking in 2D and 3D, developed by MOSAIC group @ ETH | ||
| + | * [[http:// | ||
| + | * Combination of automated single molecule tracking by several models + human check. | ||
| + | * [[http:// | ||
| + | * Stand-alone Java application for 2D tracking of epithelial cells. | ||
| + | * last update: 2010 | ||
| + | * download available by request to the authors. | ||
| + | * [[http:// | ||
| + | * native 2D tracking module in the CellProfiler | ||
| + | * object linking (or " | ||
| + | * [[http:// | ||
| + | * A plugin in Fiji | ||
| + | * 3D tracking | ||
| + | * allows selecting cost functions | ||
| + | * visualization using 3Dviewer. | ||
| + | * [[http:// | ||
| + | * optional module of Imaris. 3D tracking | ||
| + | * linking: nearest neighbor, graph theory based (like Diatrack) | ||
| + | * commercial | ||
| + | * [[http:// | ||
| + | * 3D tracking | ||
| + | * commercial | ||
| + | * [[http:// | ||
| + | * a software package, that includes 3D tracking capability. | ||
| + | * open source | ||
| + | * [[http:// | ||
| + | * Matlab m-files for linking particles, based on [[http:// | ||
| + | * [[http:// | ||
| + | * Cell Lineage analyzer (tracker) developed for C elegans. Java software. | ||
| + | * AceTree, AceBatch, SNLauncher uses ImageJ as its base. | ||
| + | * [[http:// | ||
| + | * A Python package for analyzing: | ||
| + | * movement directionality | ||
| + | * motor protein dynamics (stop-and-go style movement) | ||
| + | * kymograph | ||
| + | * not a tracking software, but useful for analysis of tracked coordinate data and kymographs. | ||
| + | * last update: 19/05/2010 | ||
| + | * [[http:// | ||
| + | * An ImageJ plugin for tracking mitochondria transport through axons. | ||
| + | * produces " | ||
| + | * last update: 04/ | ||
| + | ==== Registration ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * Command line tool for rigid and nonrigid registration of images, based on ITK (Insight Segmentation and Registration Toolkit). | ||
| + | * [[http:// | ||
| + | * An ImageJ plugin, originally made for tomography. Allows to use file describing the transformation and apply it to many stacks. | ||
| + | * [[http:// | ||
| + | * An Fiji menu item. Allows you to load 4D stack and correct for the 3D drift in the sequence. Headless version (to do the same in server) is available [[https:// | ||
| + | * A script [[https:// | ||
| + | * loads a csv file with feature point pair coordinates and does affine transformation accordingly. | ||
| + | |||
| + | ==== FCS ==== | ||
| + | |||
| + | * [[http:// | ||
| + | |||
| + | ==== Video Editing ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * Freeware for editing and compressing videos. | ||
| + | * [[http:// | ||
| + | * Command line tool for converting compression and data format. Build (win) could be found at [[http:// | ||
| + | |||
| + | |||
| + | ==== 3D Visualization ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * Commercial. | ||
| + | * Available in the ALMF, floating license. | ||
| + | * **PU** Stefan, Yury | ||
| + | * [[http:// | ||
| + | * Available in the ALMF. | ||
| + | * [[http:// | ||
| + | * part of Fiji bundle. Scriptable interface (various languages). | ||
| + | * [[http:// | ||
| + | * Ray-racing software for rendering 3D scenes. A classic software but still is powerful if you want to compile 3D animation. Does not use OpenGL (you cannot click and rotate object interactively using mouse), and outputs are 2D images. Using this tool from command-line is an efficient and a quick way of producing 3D animations. | ||
| + | * Uses original scripting language. Partially wrapped by python. | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * VTK with GUI, from Kitware. | ||
| + | * import: many. Also Tiff stack directly | ||
| + | * Single Channel | ||
| + | * last update: July 20, 2011 | ||
| + | * [[http:// | ||
| + | * Yury's recommendation. | ||
| + | * [[http:// | ||
| + | * 3D, 4D viewer. | ||
| + | * last update: Jun. 08. 2011 | ||
| + | * [[http:// | ||
| + | * 3D viewer, with some capability in image analysis. | ||
| + | * import: numbered image files (.tif, bmp. .jpg, .png), Leica (.lei), Zeiss (.lsm), IPlab (.ipl) | ||
| + | * Multi-channel capability, time series as well. | ||
| + | * export 3D models: Wavefront (.obj), VRML2.0, VTK | ||
| + | * Java based, works in Windows. Authors recommend using Parallel desktop or VMfusion on top of OSX, if you want to use it in Mac. | ||
| + | * To increase memory size, change RunImageSurferAlone.bat. " | ||
| + | * last update: Oct. 20, 2009 | ||
| + | * [[http:// | ||
| + | * " | ||
| + | * requires specific NVIDIA graphic card (GTX400 series). | ||
| + | * windows only. | ||
| + | * [[https:// | ||
| + | * Native reading of .vtk (Visualization Toolkit), .stl (Standard Tessellation), | ||
| + | * Volume rendering, thresholding and cross-sectional slicing of 3d image data | ||
| + | * Integration of the Constructive Solid Geometry-library supporting Boolean operations like union and intersection on meshes | ||
| + | * Javascript and HTML5 based: suppport of major browsers (Chrome, Firefox, Safari and Opera) | ||
| + | * CDash + Google Closure Compiler driven build system | ||
| + | * [[http:// | ||
| + | * "Four dimensional time lapse measurements are used to solve a variety of fundamental questions in developmental biology. Despite the availability of sophisticated image acquisition and object tracking software, we felt that a simple to use, interactive method for visualizing and displaying the tracked cells was lacking. To fill this gap we created Trace Pilot.\\ TracePilot is a Java-based software that executes both on Windows PCs and Macintosh computers." | ||
| + | * last update: unknown. | ||
| + | ==== Super Resolution ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * GPU-Run Analysis for STORM and PALM in ImageJ | ||
| + | |||
| + | ==== Misc Utilities ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * general mark up text converter | ||
| + | |||
| + | |||
| + | ===== Coding ===== | ||
| + | |||
| + | ==== IDE, Tools ==== | ||
| + | * [[http:// | ||
| + | * Eclipse Plugins | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * version control | ||
| + | * for windows, use [[http:// | ||
| + | * for windows, [[http:// | ||
| + | * To learn how to use Git, [[http:// | ||
| + | * [[http:// | ||
| + | * Windows desktop tool for using revision control system SVN | ||
| + | |||
| + | ==== Java Libraries ==== | ||
| + | * JAVA 6 [[http:// | ||
| + | * ImageJ [[http:// | ||
| + | * [[http:// | ||
| + | * Plugin ParticleTracker [[https:// | ||
| + | * plugin: [[http:// | ||
| + | * Fiji [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Mines Java Toolkit [[http:// | ||
| + | * MIPAV [[http:// | ||
| + | * [[http:// | ||
| + | * wrappers to commonly used libraries by researchers in the field of CV (not only openCV!) | ||
| + | * Apache Commons Math 3.0 [[http:// | ||
| + | * [[http:// | ||
| + | |||
| + | ==== C/C++ Libraries ==== | ||
| + | |||
| + | * [[http:// | ||
| + | * generic programming for computer vision: " It's a novel computer vision library that puts its main emphasize on customizable algorithms and data structures. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, | ||
| + | * **PU** Thomas Walter, involved in development as well | ||
| + | * [[http:// | ||
| + | * The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization ... VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python. | ||
| + | * Python binding is included in the Enthought package and PythonXY | ||
| + | * [[http:// | ||
| + | * FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today' | ||
| + | * [[http:// | ||
| + | * Numerical Algorithm Group: " NAG's mathematical and statistical components underpin thousands of programs and applications spanning the globe in industries as diverse as financial analysis, science and engineering, | ||
| + | |||
| + | ==== Python Modules ==== | ||
| + | * [[http:// | ||
| + | * limited to 2D, but rich filters and motion analysis modules. | ||
| + | * OpenCV [[http:// | ||
| + | * [[http:// | ||
| + | * reading and writing Tiff files in modern way (compared to PIL!) | ||
| + | * [[http:// | ||
| + | * accessing google docs and so on from command line (and python script). | ||
| + | * [[http:// | ||
| + | * Python Shell. From 0.11, you could also have inline images. | ||
| + | * typical start up of 0.10 for mayavi: " | ||
| + | * this became different in 0.11: " | ||
| + | * [[http:// | ||
| + | * IDE for development in Python. See [[http:// | ||
| + | * [[http:// | ||
| + | * 3D visualization module, openGL. Part of Enthought package, and could be installed individually. | ||
| + | * [[http:// | ||
| + | * VTK is a C++ linrary, but it could be compiled with Python and Java bindings. | ||
| + | * [[http:// | ||
| + | * Using R from Python. Since R has huge resource of math and statistics function, one could do many things efficiently. For example, [[http:// | ||
| + | * [[http:// | ||
| + | * Accessing JVM from Python. | ||
| + | * [[http:// | ||
| + | * Limited to 8-bit, but used widely. I recommend using openCV rather than PIL. | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * ParticleStats, | ||
| + | |||
| + | |||
| + | ===== Modeling and Simulation ===== | ||
| + | |||
| + | * [[http:// | ||
| + | * Virtual Cell Modeling & Analysis Software, Developed by the National Resource of Cell Analysis & Modeling (NRCAM) | ||
| + | * "The Virtual Cell is a unique computational environment for modeling and simulation of cell biology . It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Such models can be based on both experimental data and purely theoretical assumptions." | ||
| + | * [[http:// | ||
| + | * Developed in Nedelc Lab, EMBL Free Nedelc group | ||
| + | * [[http:// | ||
| + | * ODE simulation | ||
| + | * " | ||
| + | * [[http:// | ||
| + | * stochastic simulation | ||
| + | * STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm. | ||
| + | * [[http:// | ||
| + | * stochastic simulation | ||
| + | * Platform: MatLab | ||
| + | * [[http:// | ||
| + | * stochastic simualtion: stand alone | ||
| + | * "The computer program StochSim was written by Carl Firth (formerly Carl Morton-Firth) as part of his PhD work at the University of Cambridge (Morton-Firth, | ||
| + | * [[http:// | ||
| + | * compatible with StochSim | ||
| + | * "We have developed AgentCell, a model using agent-based technology to study the relationship between stochastic intracellular processes and behavior of individual cells. As a test-bed for our approach we use bacterial chemotaxis, one of the best-characterized biological systems. In this model, each bacterium is an agent equipped with its own chemotaxis network, motors and flagella. Swimming cells are free to move in a 3D environment. Digital chemotaxis assays reproduce experimental data obtained from both single cells and bacterial populations." | ||
| + | * [[http:// | ||
| + | * Platform: C/C++ code but only binaries offered. C-like scripting to interface. | ||
| + | * MCell is a modeling tool for realistic simulation of cellular signaling in the complex 3-D subcellular microenvironment in and around living cells -- what we call cellular microphysiology. At such small subcellular scales the familiar macroscopic concept of concentration is not useful and stochastic behavior dominates. MCell uses highly optimized Monte Carlo algorithms to track the stochastic behavior of discrete molecules in space and time as they diffuse and interact with other discrete effector molecules (e.g. ion channels, enzymes, transporters) heterogeneously distributed within the 3-D geometry of the subcellular environment. | ||
| + | * [[http:// | ||
| + | * Solver: " | ||
| + | * academic price: 99 euros | ||
| + | * [[http:// | ||
| + | * Simulation Tools | ||
| + | * SAL | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | |||
| + | |||
| + | |||
| + | ===== Journals, Bibs ===== | ||
| + | |||
| + | **Journals** | ||
| + | |||
| + | **Web Journals** | ||
| + | * [[http:// | ||
| + | * journal on hardware | ||
| + | * [[http:// | ||
| + | * …at Univ. Arizona | ||
| + | |||
| + | **Bibliographies** | ||
| + | |||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | * Reference search for imformatics related papers | ||
| + | |||
| + | ===== Misc ===== | ||
| + | |||
| + | **Organizations** | ||
| + | |||
| + | * [[http:// | ||
| + | * [[http:// | ||
| + | *" | ||
| + | |||
| + | **Previous Link Page** | ||
| + | |||
| + | * [[http:// | ||
| + | |||
| + | |||
| + | |||
| + | |||
mainpages/links2011.txt · Last modified: 2016/05/24 12:46 by 127.0.0.1