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--- mainpages:links2011 [2012/04/25 08:31] – kota
+++ mainpages:links2011 [2016/05/24 12:46] (current) – external edit 127.0.0.1
@@ Line 54: / Line 54: @@
   * Python Basics
-    * [[http://diveintopython.org/toc/index.html|Dive into Python]]
+    * [[http://www.whoishostingthis.com/resources/python/|Python Introduction, Resources and FAQs]]
     * [[http://openbookproject.net/thinkCSpy/|How to Think Like a Computer Scientist]]
     * [[http://www.mindview.net/Books/TIPython|Thinking in Python]]
@@ Line 99: / Line 99: @@
     * **PU** Greg Pau, Andrea Picco, Joe Barry
   * [[http://mipav.cit.nih.gov/|MIPAV(NIH)]]: a free imaging software for biological/medical research.
     * Downloadable on inquiry.
+  * [[http://www.cellcognition.org/|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++.
+    * [[https://github.com/CellCognition/cecog|github page]]
 ==== Segmentation ====
@@ Line 129: / Line 132: @@
   * [[http://www.mathworks.com/matlabcentral/fileexchange/12413|Digital Image Correlation and tracking]]
     * MatLab m-file. see also [[http://imechanica.org/node/776]]
-  * [[http://www.mosaic.ethz.ch/Downloads/ParticleTracker|ParticleTracker]]
+  * [[http://mosaic.mpi-cbg.de/?q=downloads/imageJ|ParticleTracker]]
     * ImageJ plugin for particle tracking in 2D and 3D, developed by MOSAIC group @ ETH
   * [[http://athena.physics.lehigh.edu/speckletrackerj/|Speckle TrackerJ]]
@@ Line 139: / Line 142: @@
   * [[http://www.cellprofiler.org/CPmanual/TrackObjects.html|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).
+  * [[http://fiji.sc/wiki/index.php/TrackMate|TrackMate]]
+    * A plugin in Fiji
+    * 3D tracking
+    * allows selecting cost functions
+    * visualization using 3Dviewer.
+  * [[http://www.bitplane.com/go/products/imaristrack|Imaris Track]]
+    * optional module of Imaris. 3D tracking
+    * linking: nearest neighbor, graph theory based (like Diatrack)
+    * commercial
+  * [[http://www.cellularimaging.com/products/Volocity/quantitation/|Volocity Quantitation, tracking]]
+    * 3D tracking
+    * commercial
+  * [[http://bioimageanalysis.org/index.html|ICY]]
+    * a software package, that includes 3D tracking capability.
+    * open source
+  * [[http://physics.georgetown.edu/matlab/|The Matlab Particle Tracking Code Repository]]
+    * Matlab m-files for linking particles, based on [[http://www.physics.emory.edu/~weeks/idl/| algorithm by Grier et al. coded with IDL]].
+  * [[http://waterston.gs.washington.edu/tools.html|StarryNite, AceTree, AceBatch, SNLauncher]]
+    * Cell Lineage analyzer (tracker) developed for C elegans. Java software.
+    * AceTree, AceBatch, SNLauncher uses ImageJ as its base.
+  * [[http://www.particlestats.com/|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
+  * [[http://www.bioinformatics.babraham.ac.uk/projects/difference_tracker/|Difference Tracker]]
+    * An ImageJ plugin for tracking mitochondria transport through axons.
+      * produces "tracklets".
+    * last update: 04/02/2010
 ==== Registration ====
@@ Line 151: / Line 184: @@
   * A script [[https://github.com/cmci/ijmacros/blob/master/oleg/affinetransform3Dv3.js|affinetransform3Dv3.js]]
     * loads a csv file with feature point pair coordinates and does affine transformation accordingly.
+==== FCS ====
+  * [[http://research.stowers.org/imagejplugins/|Stowers ImageJ Plugins]]
 ==== Video Editing ====
@@ Line 201: / Line 238: @@
     * 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://www.biotec.tu-dresden.de/brand/tracepilot/tracePilot.html|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.
+==== Super Resolution ====
+  * [[http://code.google.com/p/graspj/|GraspJ]]
+    * GPU-Run Analysis for STORM and PALM in ImageJ
 ==== Misc Utilities ====
@@ Line 222: / Line 266: @@
     * for windows, use [[http://code.google.com/p/msysgit/|msysgit]]
     * for windows, [[http://code.google.com/p/tortoisegit/|TortoiseGit]] is also good.
+    * To learn how to use Git, [[http://longair.net/blog/2011/04/18/a-short-introduction-to-git/|an introduction & tutorial written by Mark Longair is useful]].
   * [[http://tortoisesvn.net/|TortoiseSVN]]
     * Windows desktop tool for using revision control system SVN
 ==== Java Libraries ====
-  * JAVA 6 [[http://download.oracle.com/javase/6/docs/api/|API]]
+  * JAVA 6 [[http://download.oracle.com/javase/6/docs/api/|Javadoc]]
-  * ImageJ [[http://rsbweb.nih.gov/ij/developer/api/index.html|API]]
+  * ImageJ [[http://rsbweb.nih.gov/ij/developer/api/index.html|Javadoc]]
     * [[http://fiji.sc/cgi-bin/gitweb.cgi?p=imagej.git|Git repo]]
-    * Plugin ParticleTracker [[https://weeman.inf.ethz.ch/ParticleTracker/doc/ParticleTrackerJavaAPI/|API]]
+    * Plugin ParticleTracker [[https://weeman.inf.ethz.ch/ParticleTracker/doc/ParticleTrackerJavaAPI/|Javadoc]]
     * plugin: [[http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:3d_binary_morphological_filters:start|3Dprocessor]], [[http://cmci.embl.de/javaapi/3Dprocessor/|JavaDoc]]
-  * Fiji [[http://pacific.mpi-cbg.de/javadoc/|API]]
+  * Fiji [[http://pacific.mpi-cbg.de/javadoc/|Javadoc]]
     * [[http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git|Git Repo]]
     * [[http://www.jfree.org/jfreechart/api/javadoc/index.html|JFreeChart API]]
+    * Mines Java Toolkit [[http://inside.mines.edu/~dhale/jtk/|Javadoc]]
   * MIPAV [[http://mipav.cit.nih.gov/documentation/api/|API]]
   * [[http://code.google.com/p/javacv/|JavaCV]]