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Links revised on Mar.15, 2012

Learning | Software | Coding | Modeling | Journals & Bibs


Textbooks (web-accessible)


Tutorials: Scripting


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
      • 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
      • ImageJ bundled with R. Eclipse like interface.
      • 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
      • 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!).
  • 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.
  • MIPAV(NIH): a free imaging software for biological/medical research.
    • Downloadable on inquiry.
    • “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++.


Object Tracking

    • 2D and 3D tracking software. Originally developed for Fluorescence Speckle Microscopy.
    • Commercial
    • 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.”
    • “a free software environment for image browsing, processing and cell tracking”, programmed in Matlab and standalone executable is available.
    • “… 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.”
    • 2D cell migration tracking and intensity measurement done at the same time.
    • ImageJ plugin for particle tracking in 2D and 3D, developed by MOSAIC group @ ETH
    • Combination of automated single molecule tracking by several models + human check.
    • Stand-alone Java application for 2D tracking of epithelial cells.
    • last update: 2010
    • download available by request to the authors.
    • 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).
    • A plugin in Fiji
    • 3D tracking
    • allows selecting cost functions
    • visualization using 3Dviewer.
    • optional module of Imaris. 3D tracking
    • linking: nearest neighbor, graph theory based (like Diatrack)
    • commercial
    • 3D tracking
    • commercial
    • a software package, that includes 3D tracking capability.
    • open source
    • Cell Lineage analyzer (tracker) developed for C elegans. Java software.
    • AceTree, AceBatch, SNLauncher uses ImageJ as its base.
    • 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
    • An ImageJ plugin for tracking mitochondria transport through axons.
      • produces “tracklets”.
    • last update: 04/02/2010


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    • An ImageJ plugin, originally made for tomography.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


Video Editing

3D Visualization

  • Imaris (BitPlane): Visualization, measurements, Tracking.
    • Commercial.
    • Available in the ALMF, floating license.
    • PU Stefan, Yury
  • Volocity: 3D rendering, Visualization.
    • Available in the ALMF.
    • part of Fiji bundle. Scriptable interface (various languages).
    • 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.
    • VTK with GUI, from Kitware.
    • import: many. Also Tiff stack directly
    • Single Channel
    • last update: July 20, 2011
    • Yury's recommendation.
    • 3D, 4D viewer.
    • last update: Jun. 08. 2011
    • 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 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.
    • 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
    • “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

    • GPU-Run Analysis for STORM and PALM in ImageJ

Misc Utilities

    • general mark up text converter


IDE, Tools

Java Libraries

C/C++ Libraries

    • 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
    • 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
    • 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.

Python Modules

    • limited to 2D, but rich filters and motion analysis modules.
    • reading and writing Tiff files in modern way (compared to PIL!)
    • accessing google docs and so on from command line (and python script).
    • 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”
    • IDE for development in Python. See this page for installation.
    • 3D visualization module, openGL. Part of Enthought package, and could be installed individually.
    • VTK is a C++ linrary, but it could be compiled with Python and Java bindings.
    • Using R from Python. Since R has huge resource of math and statistics function, one could do many things efficiently. For example, see here.
    • Accessing JVM from Python.
    • 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.

Modeling and Simulation

    • 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.”
    • Developed in Nedelc Lab, EMBL Free Nedelc group
    • 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.
    • stochastic simulation
    • STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm.
    • stochastic simulation
    • Platform: MatLab
    • 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. ”
    • 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.”
    • 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.
    • 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
    • Simulation Tools
  • SAL

Journals, Bibs


Web Journals




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