Acknowledgements
The contents of the file ACKNOWLEDGEMENTS.txt is listed below.
Acknowledgements
This project incorporates code from a number of external sources, and we are
grateful to the authors for making the code available. To the best of our
knowledge this information is complete and correct; however, we apologise
for any unintentional errors and/or omissions, and will endeavour to correct
these if made aware of them.
% --------------------------------------------------------------------------- %
The CHIPS class CalcFindROIsFLIKA (and other associated classes) are based on
the algorithm described in the following paper:
- Ellefsen KL, Settle B, Parker I, Smith IF. An algorithm for automated
detection, localization and measurement of local calcium signals from
camera-based imaging. Cell Calcium. 2014 56(3):147-56.
This algorithm is also available as a standalone python package at
http://flika-org.github.io/. The original MATLAB code, which we have
modified in our implementation, was kindly provided to us by Kyle Ellefsen and
Ian Smith under the MIT License.
FLIKA - Copyright (c) 2015-2017 Kyle Ellefsen
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
% --------------------------------------------------------------------------- %
The CHIPS class CalcFindROIsCellSort (and other associated classes) are based
on the algorithm described in the following paper:
- Mukamel EA, Nimmerjahn A, Schnitzer MJ. Automated Analysis of Cellular
Signals from Large-Scale Calcium Imaging Data. Neuron. 2009 63(6):747-60.
The original MATLAB code implementing this algorithm, which we have
modified in our implementation, is available on github at
https://github.com/mukamel-lab/CellSort, and was kindly released to us by
Eran Mukamel under the GNU General Public License v3.
CellSort - Copyright (c) 2009 Eran Mukamel
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/>.
% --------------------------------------------------------------------------- %
The CHIPS function utils.motion_correction, when using the 'hmm' method (Hidden
Markov Model), uses the algorithm and a number of functions described in the
following paper:
- Dombeck DA, Khabbaz AN, Collman F, Adelman TL, Tank DW. Imaging Large-Scale
Neural Activity with Cellular Resolution in Awake, Mobile Mice. Neuron.
2007 56(1):43–57.
The original MATLAB code, which we have modified in our implementation, was
kindly released to us by David Tank, Daniel Dombeck, and Forrest Collman, under
the GNU General Public License v3.
CellSort - Copyright (c) 2009 Forrest Collman et al.
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/>.
% --------------------------------------------------------------------------- %
Although the code itself was not used directly, we are also greatful to the
authors of the following papers for releasing or otherwise making versions of
their algorithms and/or code available.
The CHIPS class CalcVelocityRadon (and other associated classes) are based
on the algorithm described in the following paper:
- Drew PJ, Blinder P, Cauwenberghs G, Shih AY, Kleinfeld D. Rapid determination
of particle velocity from space-time images using the Radon transform.
Journal of Computational Neuroscience. 2010;29(1-2):5-11
The CHIPS class CalcVelocityLSPIV (and other associated classes) are based
on the algorithm described in the following paper:
- Kim TN, Goodwill PW, Chen Y, Conolly SM, Schaffer CB, Liepmann D, et al.
Line-scanning particle image velocimetry: an optical approach for quantifying
a wide range of blood flow speeds in live animals. PLoS One. 2012;7(6):e38590
The CHIPS class CalcDiameterTiRS (and other associated classes) are based
on the algorithm described in the following paper:
- Gao Y-R, Drew PJ. Determination of vessel cross-sectional area by
thresholding in Radon space. J Cereb Blood Flow Metab. 2014;34(7):1180-7
% --------------------------------------------------------------------------- %
The following files/functions are copyright the authors (as listed) according
to the terms of the Revised BSD licence as listed at the bottom of this section
- "patchline", (c) 2014, The MathWorks, Inc., retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/36953
- "makeColorMap", (c) 2016, The MathWorks, Inc., retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/17552
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the distribution
* Neither the name of the The MathWorks, Inc. nor the names
of its contributors may be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
% --------------------------------------------------------------------------- %
The following files/functions are copyright the authors (as listed) according
to the terms of the Revised BSD licence as listed at the bottom of this section
- "sc" and its associated files, (c) 2014, Oliver J. Woodford, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/16233. We have modified
the original code in our implementation.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the {organization} nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
% --------------------------------------------------------------------------- %
The following files/functions are copyright the authors (as listed) according
to the terms of the Revised BSD licence as listed at the bottom of this section
- "inpaintn", (c) 2013, Damien Garcia, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/27994
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the distribution
* Neither the name of the RUBIC - Research Unit of Biomechanics & Imaging in Cardiology nor the names
of its contributors may be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
% --------------------------------------------------------------------------- %
The following files/functions are copyright the authors (as listed) according
to the terms of the FreeBSD licence as listed at the bottom of this section
- "bresenham", Copyright (c) 2010, Aaron Wetzler, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/28190.
- "convnfft" and related functions, Copyright (c) 2009, Bruno Luong, retrieved
from http://www.mathworks.com/matlabcentral/fileexchange/24504. We have
modified the original code in our implementation.
- "cell2csv", Copyright (c) 2004-2010, Sylvain Fiedler, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/4400.
- "GetFullPath", Copyright (c) 2010, Jan Simon, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/28249.
- "lsqnonnegvect", Copyright (c) 2016, David Provencher, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/47476.
- "mtit", Copyright (c) 2009, urs (us) schwarz, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/3218.
- "mygaussfit", Copyright (c) 2007, Yohanan Sivan, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/11733. We have modified
the original code in our implementation.
- "parsepropval", Copyright (c) 2009, Douglas M. Schwarz, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/22671. We have modified
the original code in our implementation.
- "saveastiff", Copyright (c) 2016, YoonOh Tak, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/35684. We have modified
the original code in our implementation.
- "slidefun", Copyright (c) 2015, Jos van der Geest, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/12550.
- "txtmenu", Copyright (c) 2013, Sky Sartorius, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/28285.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the distribution
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
% --------------------------------------------------------------------------- %
The following files/functions are copyright the authors (as listed) according
to the terms of the MIT licence as listed at the bottom of this section
- "boundedline", Copyright (c) 2015 Kelly Kearney, retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/27485. We have modified
the original code in our implementation.
- "publishreadme-pkg", Copyright (c) 2016 Kelly Kearney, retrieved from
https://github.com/kakearney/publishreadme-pkg. We have modified the
original code in our implementation.
- "mxdom2md.xsl", Copyright (c) 2015 Aslak Grinsted, retrieved from
https://github.com/grinsted/gwmcmc/blob/master/private/mxdom2md.xsl. We
have modified the original code in our implementation.
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
% --------------------------------------------------------------------------- %
The following files/functions are copyright the authors (as listed) according
to the terms of the Apache licence v2.0 as listed at the bottom of this section
- "cubehelix", Copyright (c) 2015 Stephen Cobeldick, retrieved from
https://www.mathworks.com/matlabcentral/fileexchange/43700.
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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% --------------------------------------------------------------------------- %
We are not aware of any particular licence terms for the following
files/functions/scripts/code snippets.
- "moving_average" by Matlab Central user 'Carlos Adrian Vargas Aguilera',
retrieved from http://www.mathworks.com/matlabcentral/fileexchange/12276.
We have modified the original code in our implementation.
- The "nansuite" package by Matlab Central user 'Jan Glaescher', retrieved from
http://www.mathworks.com/matlabcentral/fileexchange/6837. We have modified
the original code in our implementation.
- "ReadImageJROI.m", by UZH member Dylan Muir
- Portions of the function "stack_slider", by StackOverflow user 'Benoit_11',
retrieved from http://stackoverflow.com/questions/28256106/image-stack-display-in-matlab-using-a-slider.
We have modified the original code in our implementation.
- "scim_openTif.m" and "parseHeader.m", taken from ScanImage v3.8.1. Refer to
Pologruto TA, Sabatini BL, Svoboda K. ScanImage: Flexible software for
operating laser scanning microscopes. BioMed Eng OnLine. 2003;2(1):1-9.
We have modified the original code in our implementation.
% --------------------------------------------------------------------------- %
Although the code is not incorporated into CHIPS directly, and must be
downloaded separately, we are greatful to the authors of the following software
libraries and/or packages for releasing or otherwise making versions of their
code available.
The CHIPS class BioFormats uses the Bio-Formats java library and MATLAB
functions, as described in the following paper:
- Linkert M, Rueden CT, Allan C, Burel J-M, Moore W, Patterson A, et al.
Metadata matters: access to image data in the real world. The Journal of
Cell Biology. 2010 May 31;189(5):777–82. The Bio-Formats Library is
available from https://www.openmicroscopy.org/site/products/bio-formats.
The CHIPS function utils.denoise() calls a number of functions described in the
following papers:
- Azzari L, Mäkitalo M, Foi A. Optimal inversion of the Anscombe and
Generalized Anscombe variance-stabilizing transformations. Available from
http://www.cs.tut.fi/~foi/invansc/.
- Maggioni M, Sánchez-Monge E, Foi A, Danielyan A, Dabov K, Katkovnik V,
Egiazarian K. Image and video denoising by sparse 3D transform-domain
collaborative filtering. Available from http://www.cs.tut.fi/~foi/GCF-BM3D/.