Links

Links revised on Mar.15, 2012

Learning | Software | Coding | Modeling | Journals & Bibs

Textbooks (web-accessible)

• The Scienetist and Engineer's Guide to Digital Image Processing
  • All chapters downloadable
• Numerical Recipes in C
  • 2nd edition. Better updates are available in thr 3rd Ed (then not free, or library).
• Fundamentals of Image Processing (PDF)
• FreeTechbooks.com: ComputerVision
  • A list of free CV books available on the web
• FreeTechbooks.com: Signal Processings
  • A list of free SP books available on the web

Tutorials

• CMCI TextBook I: Basics
  • PDF. Learning Basics using ImageJ.
• CMCI Textbook II: ImageJ Macro Programming
  • PDF. IJ Macro from very beginning and also primer for Javascript.
• Image Analysis and processing
  • short tutorial @ National Instruments
• Image Processing Fundamentals
  • detailed hyper texts
• Digital Imaging @ Optical Microscopy
  • Detailed in Microscopy systems
• Digital Image Processing Tutorial
  • for Remote Sensing, but the principle is same. 
• Image Prosessing Learning Resources
  • ““explore with JAVA”” 2000-Oct
• UTK Mathematical Life Sciences Page for Education
  •  Practical lessons for analysis of biolgical data
• An Image Processing Workflow
  • processing tutorial for Photoshop 
• HyperStat Online Texbook
  • for treating results
• OpenGL video tutorial
  • for 3D Graphic Presentations

Tutorials: Scripting

• Jython @ Fiji
• Jython, Fiji scripting tutorial
  • Excellent Fiji+Jython tutorial by Albert Cardona.
• Javascript @ Fiji

• Python Basics
  • Python Introduction, Resources and FAQs
  • How to Think Like a Computer Scientist
  • Thinking in Python
• IP tutorial @ matplotlib site
  • Python Image Processing: importing image, plotting image and some basics.

All software, except those indicated, are freely available.
PU stands for “Power Users”, in EMBLHD.

• ImageJ: a free software for Imaging. Java application. Strong developer community with many useful plugins.
  • PU Kota Miura, Christian Tischer
• ImageJ Distributions, Variants
  • FIJI
    • Plugin-bundled distribution of ImageJ. “Fiji is Just ImageJ”,functioning also as a platform for open-source development ImageJ community.“
    • PU: Kota Miura, Christian Tischer
  • Bio7
    • ImageJ bundled with R. Eclipse like interface.
  • µManager
    • Full integration of ImageJ + Microsopy hardware control. “Complete image acquisition and microscope control package, for Windows, Mac and Linux, easy to install and configure right “out-of-the-box”, with built in functionality and user interface for most common tasks performed in the Life Science laboratory”…“Software framework for implementing advanced and novel imaging procedures, extending functionality, customization and rapid development of specialized imaging applications.”
    • PU: Kakosenen lab, Nedelec lab
  • ImageJ 2.0
    • Next generation ImageJ.
• CellProfiler: Image based High-throughput screening: “CellProfiler cell image analysis software is designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically”
  • ImageJ Macro could be used in the pipeline.
  • PU: Christian Tischer
• Matlab (mathWorks): Widely used for image analysis in biology. “MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.”. Managed by Group licenses in EMBL (ask your boss!).
  • PU: Sebastian Streichan, Alex De Marco, Wanqing Xiang, Nedelec lab
  • commercial.
    • FMATtoolbox
    • Circular Statistics Tool box
• LabView (National Instruments): Controlling machines, image processing modules.
  • Commercial.
  • PU: Christian Conrad, Ciaran Behan
• IgorPro (WaveMetrics): data analysis & plotting. Curve Fitting, Image Processing, Analysis, 3D graphics: “an extraordinarily powerful and extensible scientific graphing, data analysis, image processing and programming software tool for scientists and engineers.”
  • Commercial.
• R: statistics, plotting 2D curves, also 3D plotting.
  • RStudio: IDE for using R
  • Tutorial: see "Statistics with R"
  • PU Greg Pau, Andrea Picco, Joe Barry
• MIPAV(NIH): a free imaging software for biological/medical research.
  • Downloadable on inquiry.
• CellCognition Project
  • “Development of a fast and cross-platform image analysis framework for fluorescence time-lapse microscopy in the field of bioimage informatics.”
  • 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++.
  • github page

• Ilastik
  • Machine-learning, stand alone or CellProfiler.
• Trainable Segmentation
  • Machine-learning, Fiji plugin.. Simple version.
• Advanced Weka Segmentation
  • Machine-learning, Fiji Plugin.
• Weka Interface @@matlab
• Level Sets@Fiji
  • Fast Marching and active contour.
• Level Sets@Matlab

• DiaTrack
  • 2D and 3D tracking software. Originally developed for Fluorescence Speckle Microscopy.
  • Commercial
• CellTrack
  • 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, extensible, and cross-platform software package.”
• CellTracker
  • “a free software environment for image browsing, processing and cell tracking”, programmed in Matlab and standalone executable is available.
• Braincells
  • “… 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.”
• Quimp2
  • 2D cell migration tracking and intensity measurement done at the same time.
• Digital Image Correlation and tracking
  • MatLab m-file. see also http://imechanica.org/node/776
• ParticleTracker
  • ImageJ plugin for particle tracking in 2D and 3D, developed by MOSAIC group @ ETH
• Speckle TrackerJ
  • Combination of automated single molecule tracking by several models + human check.
• Packing Analyzer
  • Stand-alone Java application for 2D tracking of epithelial cells.
  • last update: 2010
  • download available by request to the authors.
• CellProfiler Tracking module
  • native 2D tracking module in the CellProfiler
  • object linking (or “matching” so called in CellProfiler) has three different options: overlap, distance and the linear assignment problem algorithm (after Jaqaman et. al., 2008).
• TrackMate
  • A plugin in Fiji
  • 3D tracking
  • allows selecting cost functions
  • visualization using 3Dviewer.
• Imaris Track
  • optional module of Imaris. 3D tracking
  • linking: nearest neighbor, graph theory based (like Diatrack)
  • commercial
• Volocity Quantitation, tracking
  • 3D tracking
  • commercial
• ICY
  • a software package, that includes 3D tracking capability.
  • open source
• The Matlab Particle Tracking Code Repository
  • Matlab m-files for linking particles, based on algorithm by Grier et al. coded with IDL.
• StarryNite, AceTree, AceBatch, SNLauncher
  • Cell Lineage analyzer (tracker) developed for C elegans. Java software.
  • AceTree, AceBatch, SNLauncher uses ImageJ as its base.
• ParticleStats
  • 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
• Difference Tracker
  • An ImageJ plugin for tracking mitochondria transport through axons.
    • produces “tracklets”.
  • last update: 04/02/2010

• Elastix
  • Command line tool for rigid and nonrigid registration of images, based on ITK (Insight Segmentation and Registration Toolkit).
• MultiStackReg
  • An ImageJ plugin, originally made for tomography. Allows to use file describing the transformation and apply it to many stacks.
• Correct 3D Drift
  • 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 here
• A script affinetransform3Dv3.js
  • loads a csv file with feature point pair coordinates and does affine transformation accordingly.

• Stowers ImageJ Plugins

• Virtual Dub
  • Freeware for editing and compressing videos.
• FFmpeg
  • Command line tool for converting compression and data format. Build (win) could be found at http://www.videohelp.com/tools/ffmpeg

• Imaris (BitPlane): Visualization, measurements, Tracking.
  • Commercial.
  • Available in the ALMF, floating license.
  • PU Stefan, Yury
• Volocity: 3D rendering, Visualization.
  • Available in the ALMF.
• 3Dviewer@Fiji
  • part of Fiji bundle. Scriptable interface (various languages).
• POV-ray
  • 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.
• MevisLab
• VolView
  • VTK with GUI, from Kitware.
  • import: many. Also Tiff stack directly
  • Single Channel
  • last update: July 20, 2011
• InVols
  • Yury's recommendation.
• bioView3D
  • 3D, 4D viewer.
  • last update: Jun. 08. 2011
• ImageSurfer
  • 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. ”-mx512m“ to ”-mx1024m“ or so.
  • last update: Oct. 20, 2009
• FluoRender
  • “FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly.”
  • requires specific NVIDIA graphic card (GTX400 series).
  • windows only.
• WebGL for Scientific Visualization
  • Native reading of .vtk (Visualization Toolkit), .stl (Standard Tessellation), .trk (Diffusion Toolkit), .nrrd (Single-file DICOM) and .fsm (Freesurfer) files
  • 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
• TracePilot
  • “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.

• GraspJ
  • GPU-Run Analysis for STORM and PALM in ImageJ

• Pandoc
  • general mark up text converter

• Eclipse
• Eclipse Plugins
  • JD: Java decompiler.
  • EGit: Git module for Eclipse.
  • Pydev: Python development plugin.
  • Vreapper: Vim-like editing in Eclipse
• Git
  • version control
  • for windows, use msysgit
  • for windows, TortoiseGit is also good.
  • To learn how to use Git, an introduction & tutorial written by Mark Longair is useful.
• TortoiseSVN
  • Windows desktop tool for using revision control system SVN

• JAVA 6 Javadoc
• ImageJ Javadoc
  • Git repo
  • Plugin ParticleTracker Javadoc
  • plugin: 3Dprocessor, JavaDoc
• Fiji Javadoc
  • Git Repo
  • JFreeChart API
  • Mines Java Toolkit Javadoc
• MIPAV API
• JavaCV
  • wrappers to commonly used libraries by researchers in the field of CV (not only openCV!)
• Apache Commons Math 3.0 API
  • main page

• VIGRA
  • 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, without thereby giving up execution speed. “
  • PU Thomas Walter, involved in development as well
• VTK (Visualization Tool Kit)
  • 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
• Free Image
  • 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's multimedia applications. FreeImage is easy to use, fast, multithreading safe, compatible with all 32-bit versions of Windows, and cross-platform (works both with Linux and Mac OS X). Thanks to it's ANSI C interface, FreeImage is usable in many languages including C, C++, VB, C#, Delphi, Java and also in common scripting languages such as Perl, Python, PHP, TCL or Ruby.
• NAG
  • 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, and in academia and research.

• openCV, pyhton binding
  • limited to 2D, but rich filters and motion analysis modules.
  • OpenCV Python Reference
• pylibtiff
  • reading and writing Tiff files in modern way (compared to PIL!)
• googlecl
  • accessing google docs and so on from command line (and python script).
• IPython
  • Python Shell. From 0.11, you could also have inline images.
  • typical start up of 0.10 for mayavi: “ipython -wthread”
    • this became different in 0.11: “ipython -gui=wx”
• Spyder
  • IDE for development in Python. See this page for installation.
• Mayavi.mlab
  • 3D visualization module, openGL. Part of Enthought package, and could be installed individually.
• VTK
  • VTK is a C++ linrary, but it could be compiled with Python and Java bindings.
• RPy
  • Using R from Python. Since R has huge resource of math and statistics function, one could do many things efficiently. For example, see here.
• JPype
  • Accessing JVM from Python.
• Python Imaging Library
  • Limited to 8-bit, but used widely. I recommend using openCV rather than PIL.
  • Python Imaging Library handbook
• ParticleStats
  • ParticleStats, a set of flexible program modules, which input the X and Y coordinates of particles in time, and output a wide range of motility parameters, graphs and statistical analyses. We have applied the software to the study of RNA particle motility in the Drosophila blastoderm embryo, so the output parameters are those most appropriate for motor driven transport. However, the open source program is written in Python and can be configured according to any other requirements, using appropriate programming skills.

• Vcell
  • 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.”
• CYTOSIM
  • Developed in Nedelc Lab, EMBL Free Nedelc group
• Tropical
  • ODE simulation
  • “Tropical is a software for simulation and parameter estimation of reaction-diffusion models. Based on tiff images as input, Tropical estimates reaction and diffusion coefficients of user-defined differential equation models. Therefore Tropical allows the investigation of systems with inhomogeneous distribution of molecules, making it well suited for quantitative analyses of microscopy experiments such as Fluorescence recovery after photobleaching (FRAP).” free of charge for academic use after signing a license agreement.
• STOCKS
  • stochastic simulation
  • STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm.
• Exact Stochastic Simulations
  • stochastic simulation
  • Platform: MatLab
• Stochsim
  • 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, 1998). It was developed as part of a study of bacterial chemotaxis as a more realistic way to represent the stochastic features of this signalling pathway and also as a means to handle the large numbers of individual reactions encountered (Morton-Firth & Bray, 1998; Morton-Firth et al., 1999). The program now provides a general purpose biochemical simulator in which individual molecules or molecular complexes are represented as individual software objects. Reactions between molecules occur stochastically, according to probabilities derived from known rate constants. An important feature of the program is its ability to represent multiple post-translational modifications and conformational states of protein molecules. / StochSim consists of a platform-independent core simulation engine encapsulating the algorithm described above and a separate graphical user interface. ”
• AgentCell (Digital E. Coli)
  • 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.”
• MCell
  • 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.
• Berkley Madonna
  • Solver: “Berkeley Madonna is arguably the fastest, most convenient, general purpose differential equation solver available today. It is relatively inexpensive and runs on both Windows and Mac OS. Developed on the Berkeley campus under the sponsorship of NSF and NIH, it is currently used by academic and commercial institutions for constructing mathematical models for research and teaching.”
  • academic price: 99 euros
• Andrea Emilio Rizzol's Link
  • Simulation Tools
• SAL
  • source code repositories
  • discrete methods and related tools
  • optimization
  • Scientific data processing and visualization archives
  • Computer graphics, images and signals: Processing and Visualization

Journals

Web Journals

• Advanced Imaging Pro
  • journal on hardware
• Imaging Related free publication Links
  • …at Univ. Arizona

Bibliographies

• The Collection of Computer Science Bibliographies
• CiteSeer
  • Reference search for imformatics related papers

Organizations

• ELMI (European Light Microscopy Initiative))
• EMIL (European Molecular Imaging Laboratories) 
  • “Molecular Imaging Laboratories for combating cancer. EMIL coordinates research efforts in Molecular Imaging of Cancer in Europe of 59”

Previous Link Page

• http://cmci.embl.de/mainpages/links