The OCT Volume Averager plugin registers and averages optical coherence
tomography (OCT) volume datasets that are acquired by repeated scanning
from a single eye to improve the detection of fine detail. The plugin relies
on the TurboReg and StackReg plugins to perform image registration. OCT
Volume Averager is most useful for efficient processing of input data that
are organized to include repeated scans from one or more eyes in a single
folder. However, it also accepts data opened in ImageJ/Fiji. Currently the
plugin has been tested on OCT volumes acquired with a Bioptigen Envisu R2200
UHR-SDOIS instrument and includes the Bioptigen OCT Reader plugin for ImageJ
to convert Bioptigen *.oct files to *.tif format. OCT Volume Averager may be
applied in principle to repeated OCT volume scans obtained in *.tif format
from other instruments.

The TurboReg and StackReg plugins were developed by P. Thévenaz and
coworkers.  See the following websites for more information:
http://bigwww.epfl.ch/thevenaz/turboreg/
http://bigwww.epfl.ch/thevenaz/stackreg/

The OCT_Reader plugin for ImageJ was developed by Bioptigen:
Copyright 2010 Bioptigen, Inc.
Author: Bradley Bower

All other code was developed at The Jackson Laboratory:
Copyright 2013-2014 The Jackson Laboratory.
Authors: Keith Sheppard, Mei Xiao and Mark Krebs

OCT Volume Averager is citeware and may be used under the terms of the
Attribution-NoDerivatives International License as published by Creative
Commons, either version 4.0 of the License, or (at your option) any later
version, with the following exceptions. Use in source and binary forms are
permitted provided that the following conditions are met:

* Any publications (e.g. academic reports, papers, other disclosure of
  results) containing or based on data obtained with the use of this
  software will acknowledge its use by citing the following:

        P. Thévenaz, U.E. Ruttimann, M. Unser. 1998. A Pyramid Approach to
        Subpixel Registration Based on Intensity. IEEE Transactions on Image
        Processing. 7(1): 27-41. DOI:10.1109/83.650848. This paper is available
        on-line at http://bigwww.epfl.ch/publications/thevenaz9801.html; other
        relevant on-line publications are available at
        http://bigwww.epfl.ch/publications/)

        M.P. Krebs, M. Xiao, K. Sheppard, W. Hicks, P.M. Nishina. 2016.
        Bright-Field Imaging and Optical Coherence Tomography of the Mouse
        Posterior Eye. Methods in Molecular Biology. 1438:395-416.
        DOI:10.1007/978-1-4939-3661-8_20

* Use of source code or binary form is for research purposes only.

* No redistributions of the source code or binary form are permitted without
  written permission of the copyright holders; however, should redistribution
  be permitted upon receipt of written permission, all source code and binary
  form must reproduce the above copyright notice, this list of conditions and
  the following disclaimers in the documentation and/or other materials
  provided with the distribution.

* Neither the name of OCT Volume Averager 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 OCT VOLUME AVERAGER DEVELOPMENT TEAM 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.

You should have received a copy of the Creative Commons
Attribution-NoDerivatives 4.0 International License along with this program.
If not, see <https://creativecommons.org/licenses/>.
