License
Contents
License¶
nextPYP is distributed under the open-source BSD 3-Clause license.
BSD 3-Clause License¶
Copyright (c) 2023, Alberto Bartesaghi
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. 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.
3. Neither the name of the copyright holder 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.
Dependencies¶
nextPYP uses functionality from IMOD, cisTEM, CTFFIND4, AreTomo2, MotionCor3 and Topaz.
The corresponding licenses are reproduced below.
cisTEM and CTFFIND4 license¶
Copyright © 2023 Howard Hughes Medical Institute
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 HHMI 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.
IMOD license¶
IMOD Version 4.11 Copyright Notice and Credits
--------------------------------------------------------------------------
Except as noted, ALL SOFTWARE LISTED IS Copyright (C) 1994-2020
by the Regents of the University of Colorado.
All portions of IMOD, except as noted below, are open source under the
General Public License (GPL) version 2.0. A copy of this license is in the
file GPL.txt. (All license files referred to here are in the directory
'licenses' in the binary distribution or 'dist' in the source code.) The
libraries written entirely in C/C++ are released under the Lesser GPL (see
LGPL.txt). Software may be modified and redistributed under the terms of
these licenses. The source can be found at
http://bio3d.colorado.edu/imod/nightlyBuild
and
http://bio3d.colorado.edu/imod/openSource
THIS SOFTWARE AND/OR DOCUMENTATION IS PROVIDED WITH NO WARRANTY,
EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTY OF
MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE.
Programs were written by David Mastronarde, James Kremer, Rick
Gaudette, Sue Held, Quanren Xiong, and John Heumann at the University
of Colorado, some based on work and libraries from the MRC. We thank David
Agard and Hans Chen for the original MRC source code, Wah Chiu for a Unix
version of low-level MRC file routines used in the FORTRAN parts, and Chuck
Robertson for much work on the port to Linux.
The program nad_eed_3d by Achilleas Frangakis and Reiner Hegerl is
copyright Max-Planck-Institut for Biochemistry, Martinsried, Germany.
The LSQR routine by Michael Saunders is used in some programs. IMOD uses a
C version of LSQR and some BLAS routines from the BCLS package of Michael
Friedlander, which are covered by the Lesser GPL (see LGPL.txt).
IMOD uses a subset of the LAPACK routines developed at Univ. of Tennessee,
Univ. of California Berkeley, NAG Ltd., Courant Institute, Argonne National
Lab, and Rice University. They are copyrighted by the University of
Tennessee and covered by a BSD-style license (see LAPACK.txt). IMOD also
uses a subset of the BLAS routines, developed by: Jack Dongarra, Argonne
National Lab; Jeremy Du Croz, NAG Ltd.; Iain Duff, AERE Harwell; Richard
Hanson, Sandia National Labs; and Sven Hammarling, NAG Ltd.
The program imodwincpu was adapted from code obtained from
www.codeproject.com and written by Dudi Abramov. It is excluded from the
GPL license and is covered exclusively by the Code Project Open License (see
CPOL.html).
Routines for computing some statistical functions were adapted from
S. J. Zhang and J. M. Jin, Computation of Special Functions. New York: John
Wiley & Sons, 1996 and are copyrighted by the authors and publisher.
Andrew Noske (originally at the University of Queensland, Australia, then at
the University of California, San Diego) contributed the beadhelper,
drawingtools, interpolator, namewizard, and stereology plugins. See the help
displayed by those plugins for acknowledgements of funding for his work.
Jane Ding at California Institute of Technology contributed the Grab with Note
plugin.
The isosurface display in 3dmod uses contouring and surface smoothing
modules from Chimera, developed at the Resource for Biocomputing,
Visualization, and Informatics at the University of California, San
Francisco, supported by NIH/NCRR grant P41-RR01081.
RAPTOR was developed by Fernando Amat, Farshid Moussavi, and Mark Horowitz
at Stanford University and is copyrighted by them. It is covered by the
license in RAPTORlicense.txt. It uses three libraries, parts of which are
included in the IMOD source code distribution:
OpenCV (http://sourceforge.net/projects/opencvlibrary/),
covered by the license in OpenCV.txt,
SuiteSparse (http://www.cise.ufl.edu/research/sparse/SuiteSparse/),
covered by the licenses in CSparse.txt and LGPL.txt, and
Stair Vision Library (http://sourceforge.net/projects/stairvision/),
covered by the license in StairVision.txt.
The warping library uses modules from Pavel Sakov's 'nn' package, which are
copyrighted by Sakov and CSIRO, and covered by the license in nn.txt. The
library also uses code from Ken Clarkson's 'hull' program, which is
copyrighted by AT&T and covered by the license in hull.txt.
Routines for solving 3x3 eigenvectors are copyrighted by Joachim Kopp and
covered by the LGPL license.
The ctffind library was adapted from the ctffind program of Alexis Rohou and
Nikolaus Grigorieff, which is Copyright (c) 2018, Howard Hughes Medical
Institute, and is covered by the Janelia Research Campus Software License
1.2.
Mauro Maiorca, at the Biochemistry & Molecular Biology Department, Bio21
Institute, University of Melbourne, Australia, contributed the preNAD and
preNID programs. His work was supported by funding from the Australian
Research Council and the National Health and Medical Research Council. preNAD
and preNID use recursive line filter routines from Gregoire Malandain, covered
by version 3 of the GPL (see GPL-3.0.txt).
IMOD uses TIFF libraries which are Copyright (c) 1988-1997 Sam Leffler
and Copyright (c) 1991-1997 Silicon Graphics, Inc. (see TIFF.txt).
Because IMOD uses the libjpeg library, this software is based in part on the
work of the Independent JPEG Group. IMOD also uses the zlib library, which is
Copyright 1995-2010 by Jean-loup Gailly and Mark Adler.
IMOD may use FFTW libraries which are Copyright (c) 1997--1999 Massachusetts
Institute of Technology, written by Matteo Frigo and Steven G. Johnson, and
covered by version 2 of the GPL.
IMOD uses HDF5 libraries which are Copyright 1998-2006 by the Board of
Trustees of the University of Illinois and Copyright 2006-2014 by The HDF
Group and covered by the license in HDF5.txt.
The module gcvspl.c is based on an f2c translation of gcvspl.f, which was
obtained from http://www.netlib.org. gcvspl.f was written by H.J. Woltring
based on routines in Lyche et al. (1983) and other sources as documented in
gcvspl.c.
IMOD includes a copy of the Mini-XML library which is Copyright 2003-2016 by
Michael R. Sweet and is covered by the modified Library GPL in Mini-XML.txt
This work is supported by NIH/NIGMS grant GM125074 to David Mastronarde.
Contact: mast at colorado dot edu
www: http://bio3d.colorado.edu/imod/index.html
University of Colorado, Dept. of MCD Biology, 347 UCB, Boulder, CO 80309
AreTomo2 and MotioCor3 license¶
Copyright 2023 Chan Zuckerberg Institute for Advanced Biological Imaging
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list
of conditions and the following disclaimer.
2. 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.
3. Neither the name of the copyright holder 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.
Topaz license¶
Topaz is distributed under the GNU General Public License v3.0.