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Using the image_analyser
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The image analyser 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 Parameters
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ALPHA": 0.03,       # a gliding threshold to identify objects. Typical values are between 0.01 and 0.08
ELONGATION" : 0.85,  # threshold in fraction of maximum intensity, at which the stick gets elongated
STEP LENGTH" : 5, # number of pixels by which to elongate
LENGTH PROTOTYPE": 25, # approximate average length of a stick (px)
MINIMAL LENGTH": 5, # minimal length of seeds to detect (number of pixels)
MIN INTENSITY" : 0, # for 16bit image
BENDING ANGLE" : 5,# maximum angle at which the MT extensions are allowed to fluctuate
SCAN LENGTH FACTOR" : 1.2, # factor by which to elongate current length in next frame
TEST LENGTH" : 20, #number of pixels to scan for extension
END BENDING THRESHOLD": 0.8, # minimum intensity to change direction (allow for bending extensions)
MEDIAN" : 6, # Median filter. Helps detection if beads or small objects are in the field of view.
DUAL COLOR": True, # images containing 2 color layers
STOP" : False, # stop and show detected objects
 FILE": "./", # image file to be evaluated
DRIFT": "",# file containing reference coordinates of drift in x,y form
GUI" :  True, #show GUI

B 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

C 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


