=============================
**Using the tracking module**
=============================

The tracker module was designed to detect and track objects in movies. The intention was to provide a framework in which microscopy data can be evaluated easily.
The program is part of SLOTH, which contains all necessary modules. 

A Scope
=======

The module was designed and tested on dynamic microtubule assays that were imaged using TIRF. 
Other possible applications are DNA stretching assays, depolymerization assays or other images or image stacks containing stick-like objects.

(http://en.wikipedia.org/wiki/Microtubule)

B Parameters of the tracker module
==================================


+-------------------------+----------------------------------------------------------------+
|Parameter                |                              Description                       |
+=========================+================================================================+ 
| ALPHA                   | a gliding threshold to identify objects                        |                  
+-------------------------+----------------------------------------------------------------+
| ELONGATION              | threshold in fraction of maximum intensity for elongation      |              
+-------------------------+----------------------------------------------------------------+
| STEP LENGTH             | number of pixel per elongation step                            |
+-------------------------+----------------------------------------------------------------+
| LENGTH PROTOTYPE        | initial guess of the average length of an object in pixel      |       
+-------------------------+----------------------------------------------------------------+
| MINIMAL LENGTH          | minimal length of objects to detect (number of pixel)          |        
+-------------------------+----------------------------------------------------------------+
| MIN INTENSITY           | minimal intensity an object needs to have to be identified     |          
+-------------------------+----------------------------------------------------------------+
| BENDING ANGLE           | maximum angle at which extensions are allowed to fluctuate     |           
+-------------------------+----------------------------------------------------------------+
| SCAN LENGTH FACTOR      | how much further to scan for an end                            |    
+-------------------------+----------------------------------------------------------------+
| TEST LENGTH             | number of pixel to scan for extension                          |            
+-------------------------+----------------------------------------------------------------+
| END BENDING THRESHOLD   | intensity of bending extensions, as fraction of total intensity|  
+-------------------------+----------------------------------------------------------------+
| MEDIAN                  |  Median filter                                                 |
+-------------------------+----------------------------------------------------------------+
| DUAL COLOR              | images containing two color layers                             |              
+-------------------------+----------------------------------------------------------------+
| STOP                    |stop & show detected objects after identif. i.e.after 1st frame |       
+-------------------------+----------------------------------------------------------------+
| FILE                    | image file to be evaluated                                     |                    
+-------------------------+----------------------------------------------------------------+
| DRIFT                   | file containing reference coordinates of drift in x,y form     |                   
+-------------------------+----------------------------------------------------------------+
| GUI                     |show GUI (uncheck for use in the terminal)                      |                    
+-------------------------+----------------------------------------------------------------+
| SHIFT                   | multiply green layer by shift to equalize intensity differences| 
+-------------------------+----------------------------------------------------------------+
	

C Using the terminal
====================

All parameters can be specified in the terminal, by substituting a space " " with an underscore "_".

python image_analyser.py STOP=1 GUI=1 ../Test/movie.nd2

D Supported Formats
===================

.TIF and .nd2 (version 4.0) are supported at this time. The .TIF support is thanks to tifffile.py, provided by Christoph Gohlke.
http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html