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Fluorescence Imaging Toolbox for ISET
This project forked from hblasins/fitoolbox
Fluorescence Imaging Toolbox for ISET
Fluorescence Imaging Toolbox for Image Systems Engineering Toolbox (fiToolbox for ISET) This toolbox serves as an extension of the Image Systems Engineering Toolbox (ISET) which provides a set of functions to simulate scenes with fluorescent components. The fiToolbox also implements several reflectance and fluorescence separation and estimation algorithms. A copy of ISET is not needed to run these algorithms. If you use this code in your work, please cite Henryk Blasinski, Joyce Farrell and Brian Wandell - "Simultaneous reflectance and fluorescence spectra estimation" 2016 (https://arxiv.org/abs/1605.04243) 0. License ---------- The code is provided as is. You are free to use and modify the code in non-commercial and research applications. If you are interested in commercial applications, please contact us as the method and apparatus is a subject of a US Patent 20,160,116,410. 1. Installation --------------- To install the fiToolbox run fiToolboxInit function. This function adds all the relevant directories to MATLAB path. Make sure that the additional dependencies (see below) are on the MATLAB path. 2. Dependencies (required) -------------------------- a. Image Systems Engineering Toolbox (ISET) (http://www.imageval.com). b. cvx Convex Optimization toolbox for Matlab (www.cvxr.com). 3. Dependencies (optional) -------------------------- The following code is used by some data plotting scripts and are not required to simulate or analyze reflectance and fluorescence. a. Barwitherr function from Matlab File exchange. (http://www.mathworks.com/matlabcentral/fileexchange/30639-barwitherr-errors-varargin). b. Code accompanying the Computational Colour Science using Matlab from Matlab File exchange. (http://www.mathworks.com/matlabcentral/fileexchange/40640-computational-colour-science-using-matlab-2e) 4. Sample data -------------- The sample inputs to our algorithms as well as the results of the analyses can be downloaded from Stanford's Digital Repository: http://purl.stanford.edu/xc528jd5098 The zip file downloaded from the above side contains two directories: 'data' with raw input data from real captures and simulations and 'results' storing algorithm outputs. Please place these two folders directly in the fiToolbox root folder.
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