README 
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This package contains code for counting glomeruli in Light-Sheet microscopy images
of kidney. Full details of the alogrithm can be found in the paper 
Klingberg et al. (2017) Fully Automated Evaluation of Total Glomerular Number and 
Capillary Tuft Size in Nephritic Kidneys Using Lightsheet Microscopy,
J. Am. Soc. Nephrol., 28: 452-459. 

If any part of this code is used for academic purposes please cite the paper
above.

Contents
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analyze_kidney.py:
	Script for counting glomeruli
compute_volume.py:
	Script for computing the volume of the kidney
LICENCE:
	Licencing details of this software (BSD License 2.0).
include/boost.py:
	functions for parallel image processing
include/filelib.py:
	functions for working with files

Requirements:
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Python 2.7+:
	Code is developed and tested using Python 2.7.3
numpy:
	Tested on numpy 1.9.1. http://www.numpy.org/
Scipy.ndimage:
	Tested on scipy.ndimage 2.0 http://www.scipy.org/
mahotas:
	Tested on Mahotas 1.0.3
argparse:
	Tested on argparse 1.1
pandas:
	Tested on pandas 0.15.2 http://pandas.pydata.org/

Usage:
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To count glomeruli:
	Run in command line: ``python analyze_kidney.py -i settings.csv``
To compute kindney volume:
	Run in command line: ``python compute_volume.py -i settings.csv``