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	  Balanced super-resolution optical fluctuation imaging (bSOFI)
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** Contents

	1. Overview
	2. Requirements
	3. Installation
	4. Copyright
	5. Warranty
	6. History
	7. Download
	8. Trademarks

** Publisher

	Marcel Leutenegger				marcel.leutenegger@a3.epfl.ch
	Stefan Geissbhler				stefan.geissbuehler@alumni.epfl.ch

	cole Polytechnique Fdrale de Lausanne EPFL
	Laboratoire d'Optique Biomdicale LOB
	Btiment BM 5.142
	Station 17
	CH-1015 Lausanne
	Switzerland


1. Overview

	Super-resolution optical fluctuation imaging (SOFI) is an analysis method to gather
	super-resolved information from a sequence of diffraction-limited optical microscope
	images [1]. This toolbox contains the core tools for analyzing image sequences. It
	features extensions for balancing the SOFI image brightness and for extracting some
	functional information as described in our recent publication [2].

	SOFICUMULANTS uses the MATLAB toolbox for parallel computing on CUDA capable graphics
	cards (GPU) if available. The parallel GPU toolbox is featured since MATLAB R2012a
	and exploits the high computation performance of NVIDIA GPUs.

	A function summary is given in CONTENTS and useful implementation details are found
	in SOFIGRIDS. EXAMPLE shows the analysis of an image sequence.


    [1]	T. Dertinger, R. Colyer, G. Iyer, S. Weiss, J. Enderlein, "Fast, background-free, 3D
	super-resolution optical fluctuation imaging (SOFI)," Proceedings of the National
	Academy of Sciences of the United States of America 106: 2228722292 (2009).

    [2]	S. Geissbuehler, N. L. Bocchio, C. Dellagiacoma, C. Berclaz, M. Leutenegger,
	Theo Lasser, "Mapping molecular statistics with balanced super-resolution
	optical fluctuation imaging (bSOFI)," Optical Nanoscopy 1:4 (2012).


2. Requirements

	 MATLAB R2012a or newer (previous versions require modifications).
	 A CUDA capable graphics card (GPU) is highly recommended.
	 At least 1GB RAM; 4GB or more is recommended.


3. Installation

	Unpack the archive and add the SOFI folder to the MATLAB path.


4. Copyright

    Copyright  2012 Marcel Leutenegger et al, cole Polytechnique Fdrale de Lausanne,
    Laboratoire d'Optique Biomdicale, BM 5.142, Station 17, 1015 Lausanne, Switzerland.
	
	This program is free software: you can redistribute it and/or modify
	it under the terms of the GNU General Public License as published by
	the Free Software Foundation, either version 3 of the License, or
	(at your option) any later version.

	This program is distributed in the hope that it will be useful,
	but WITHOUT ANY WARRANTY; without even the implied warranty of
	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
	GNU General Public License for more details.

	You should have received a copy of the GNU General Public License
	along with this program.  If not, see <http://www.gnu.org/licenses/>.


	See 'FILES' for a list of the original package contents.


5. Warranty

	Any warranty is strictly refused and you cannot anticipate any financial or
	technical support in case of malfunction or damage; see the copyright notice.

	Feedback and comments are welcome. We will try to track reported problems and
	fix bugs.


6. History

   April 10, 2013
	Version 1.2 released under GNU GPL version 3.

   March 23, 2015
	Improved parameter estimation and SOFI simulation.

   April 2, 2015
	Compatibility workaround for MATLAB installations without parallel computation
	toolbox.


7. Download

	This toolbox is available on the authors webpage(s).


8. Trademarks

	MATLAB is a registered trademark of The MathWorks. Other product or brand
	names are trademarks or registered trademarks of their respective holders.
