mainpages:links2011
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
mainpages:links2011 [2012/04/26 08:55] – kota | mainpages:links2011 [2016/05/24 12:46] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 54: | Line 54: | ||
* Python Basics | * Python Basics | ||
- | * [[http://diveintopython.org/toc/index.html|Dive into Python]] | + | * [[http://www.whoishostingthis.com/resources/ |
* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
Line 99: | Line 99: | ||
* **PU** Greg Pau, Andrea Picco, Joe Barry | * **PU** Greg Pau, Andrea Picco, Joe Barry | ||
* [[http:// | * [[http:// | ||
- | * Downloadable on inquiry. | + | * 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 ==== | ==== Segmentation ==== | ||
Line 129: | Line 132: | ||
* [[http:// | * [[http:// | ||
* MatLab m-file. see also [[http:// | * MatLab m-file. see also [[http:// | ||
- | * [[http://www.mosaic.ethz.ch/Downloads/ParticleTracker|ParticleTracker]] | + | * [[http:// |
* ImageJ plugin for particle tracking in 2D and 3D, developed by MOSAIC group @ ETH | * ImageJ plugin for particle tracking in 2D and 3D, developed by MOSAIC group @ ETH | ||
* [[http:// | * [[http:// | ||
Line 139: | Line 142: | ||
* [[http:// | * [[http:// | ||
* native 2D tracking module in the CellProfiler | * native 2D tracking module in the CellProfiler | ||
- | * object linking (or " | + | * 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/ | ||
+ | * [[http:// | ||
+ | * An ImageJ plugin for tracking mitochondria transport through axons. | ||
+ | * produces " | ||
+ | * last update: 04/ | ||
==== Registration ==== | ==== Registration ==== | ||
Line 151: | Line 184: | ||
* A script [[https:// | * A script [[https:// | ||
* loads a csv file with feature point pair coordinates and does affine transformation accordingly. | * loads a csv file with feature point pair coordinates and does affine transformation accordingly. | ||
+ | |||
+ | ==== FCS ==== | ||
+ | |||
+ | * [[http:// | ||
==== Video Editing ==== | ==== Video Editing ==== | ||
Line 201: | Line 238: | ||
* Integration of the Constructive Solid Geometry-library supporting Boolean operations like union and intersection on meshes | * 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) | * Javascript and HTML5 based: suppport of major browsers (Chrome, Firefox, Safari and Opera) | ||
- | * CDash + Google Closure Compiler driven build system | + | * 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 ==== | ==== Misc Utilities ==== | ||
Line 222: | Line 266: | ||
* for windows, use [[http:// | * for windows, use [[http:// | ||
* for windows, [[http:// | * for windows, [[http:// | ||
+ | * To learn how to use Git, [[http:// | ||
* [[http:// | * [[http:// | ||
* Windows desktop tool for using revision control system SVN | * Windows desktop tool for using revision control system SVN |
mainpages/links2011.txt · Last modified: 2016/05/24 12:46 by 127.0.0.1