EMBL CMCI Links

EMBL-CMCI Links (last update 31.Oct.2008)

Contents
	Learning web resources related to image processing and analysis.
	Software Lists of various imaging tools and users
	Modeling / Simulations
	Coding: language
	Coding: libraries
	Misc
	CMCI Alumni

Learning Digital Image Processing and Analysis

Textbooks	The Scienetist and Engineer's Guide to Digital Image Processing --> All chapters downloadable
	Numerical Recipes in C --> All chapters downloadable
	Fundamentals of Image Processing --> downloadable pdf


Web Tutorials	Image Analysis and processing --> short tutorial @ National Instruments
	Image Processing Fundamentals --> detailed texts.
	Digital Imaging @ Optical Microscopy -->
	Digital Image Processing Tutorial --> for Remote Sensing, but the principle is same.
	Image Prosessing Learning Resources --> "explore with JAVA" (10.2000)
	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 tutorial --> for 3D Graphic Presentations

Web Journal	Advanced Imaging Pro -->
	Imaging Related free publication Links -->
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"

Software (28.08.2007)
see also Links in NIH (though the last update: 2001), or "Internet Analysis Registry".

The skills and experience of each user will be indicated in accordance with Karate ranking (white to black)

Name

Availability in EMBL Heidelberg

Users in EMBL

ImageJ (NIH)
--> a free software for Imaging. Java application.

PlugIn Bundles

EMBL ImageJ	Extended Plugin Bundle of WCIF, compiled by Arne Seits @ ALMF
WCIF	A Plugin Bundle: contained Plugins are listed in this page. A good manual explaining about each plugin is also asociated, which can be found directly at the web site.

Microsopy hardware control

μManager

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

"Micro-Manager is packaged as an ImageJ plug-in and contains a copy of the entire ImageJ application, together with the Java run-time engine. Starting Micro-Manager will automatically start ImageJ as well. If you already use ImageJ and have it installed on your machine beforehand, the original installation will not be affected."

PlugIn development

Eclipse and ImageJ	How to configure Eclipse for developing ImageJ
ImageJ PlugIns page at source forge	The ImageJ Plugins project is a source of custom plugins for the ImageJ software package. ImageJ is a public domain image processing and analysis program developed in Java.

Useful ImageJ Plug-ins

Particle Tracker	for tracking fluorescence spots. data output is a bit complicated.
MTrackJ	Another tracking plugin. Initialization by user is required.
LOCI	importing various microsope company formats (last update 02.11.06)

View5D	multidimensional image sequence viewer
Tomo-J	3D reconstruction, tomography

Free

Kota Miura
Philippe Girard (PlugIn developer)
Stefan Terjung
Arne Seits
Julien Collombeli
Felipe Mora-Bermúdez (now in Dresden)

IgorPro (WaveMetrics)
--> 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."

ALMF

Kota Miura (*)
Jerome Solon
Philippe Girard
Stelzer Group

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."

   RyTrack
       --> Colloid Particel Tracking. IDL or MatLab.

   CellTracker
        --> "a free software environment for image browsing, processing and cell tracking"

group licenses

Francois Nedelec(*)
Jeronme Solon
Francesco Pampaloni
Julien Collombeli
Chaitanya Athale
Philippe Girard
Sebastian Streichan
Stelzer Group

IDL
-->Data Visualization, analysis

ALMF

MIPAV (NIH)
--> a free imaging software for biological research

Downloadabe on inquiry (free)

-- someone using?

Imaris (Bitplane)
--> Visualization, Tracking

ALMF, floating

Stefan Terjung (*)

LabView (National Instruments)
--> controlling machines, image processing modules

(Urban Liebel)
Cihan Cetin
Julien Collombeli
Stelzer Group

IMOD

Free

Johanna Höög

Amira

Achilleas Frangakis

Heurisko
--> Image Processing Tool Box

R
-->Statistical Computing, 3D graphics

Free

BioimageXD
--> Good tool for creating 3D graphics & Animation. Still under primodial development towards processing and analysis.

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"

Free

DiaTrack
2D and 3D tracking software. Originally developed for Fluorescence Speckle Microscopy.

CellTracker
"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. "

Free

Braincells

manual tracker

Free

Modeling /Simulations

CYTOSIM
--> Modeling and Simulations

Free

Francois Nedelec

Berkeley 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

see also

Andrea Emilio Rizzoli's Links

SAL: Numerical Analysis: source code repositories

SAL: Numerical Analysis: discrete methods and related tools

SAL: Numerical Analysis: Optimization

SAL: scientific data processing and visualization: libraries

Coding: languages

Coding: Image Procesing and Analysis Language and Libraries

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. "

Free

Thomas Walter

Python

learning

--> see Python Imaging Library Handbook.

for learning --> Dive into Python or How to think like a computer scientist.

more advanced --> Thinking in Python.

IDE --> Pydev (eclipse plugin)

modules

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."

Free

Chaitanya Athale

Visualization Tool Kit (VTK)

" 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. "

Free

FreeImage

" 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. "

Free

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. "

... and also check other links

SAL: Computer Graphics, Image and Signals: Procesing & Visualization

Misc

Tools	Codec Central (Index of Video Cordecs)

CMCI Alumni
members worked together in EMBL and now in elsewhere...

Julien Mozziconacci (2004-2006)