Welcome to the MorphoJ User's Guide web pages. This collection of web pages is intended to provide the essential information on the use of the MorphoJ package and on the methods implemented in it. For more thorough information, the reader is referred to the introductory books in the area of geometric morphometrics and to original publications of methods.
MorphoJ is a program package for geometric morphometric analysis for two- and three-dimensional landmark data. Further information on the program and its availability can be obtained from the MorphoJ home page.
MorphoJ is written in pure Java and is being released for
Microsoft Windows, Apple Macintosh (from OS X version 10.11, "El
Capitan", onward), and Ubuntu Linux. From version 1.08 of MorphoJ,
the distribution is as self-contained app packages for these
operating systems, so that an external Java runtime environment on
the user's computer is no longer required.
The Java version used is the Eclipse Temurin OpenJDK (https://adoptium.net/).
This version can be freely used and freely distributed.
According to the computing platform used, the appearance of the user interface will vary somewhat from the screen shots shown in this documentation, which have been produced in part on the Windows XP operating system (now obsolete), and partly under various variants of Mac OS X.
MorphoJ is a program that is designed for the analysis of actual biological data. Therefore, some choices have been made that help practitioners, but may not be ideal for analyzing simulated data with extremely large variation in shape.
MorphoJ is available freely for use in education and research. While it is permitted for you to provide copies of MorphoJ to others, it might be more helpful if you give them the link to the MorphoJ home page, because this will enable them to update the program when new versions will become available in the future.
If you use MorphoJ for research that is to be published, please cite it as follows:
C. P. Klingenberg. 2011. MorphoJ: an integrated software package for geometric morphometrics. Molecular Ecology Resources 11: 353-357.
doi: 10.1111/j.1755-0998.2010.02924.x
PDF
file of this paper.
MorphoJ is a program for the analysis of landmark data. It therefore does not contain methods for the analysis of outline data or for the conversion of outlines to series of semi-landmarks.
Moreover, MorphoJ does not support the acquisition of landmark coordinates. Other software for that purpose is readily available elsewhere (e.g. see the morphometrics web site at Stony Brook).
The MorphoJ User's Guide is intended to provide information about the commands available in the various menus and the graphical user interfaces. Accordingly, it is organized mainly according to the menus available.
The User's Guide is not primarily intended as a tutorial, and therefore contains only rudimentary explanations of the sequence of the analyses. It is planned that tutorials for certain analyses will be developed and published on the web at a later time.
In addition to Java OpenJDK Standard Edition, version 17, this program is based on a range of software resources that were used to write and deploy the program or that are incorporated into the MorphoJ distribution to perform some of its functions. These are as follows:
All of these resources are available for free through the links indicated in the list above.
I am most grateful to the developers of these software tools for producing them and making them available to the community. Without these resources, MorphoJ would not have been possible or would not have its full functionality.
The idea of writing MorphoJ was stimulated by the members of my lab and by the participants of morphometrics workshops and courses that I have taught. I thank them and numerous friends and colleagues for testing the various early versions of MorphoJ, providing data sets that stretched its limits (or worse!), making suggestions for what should be included in MorphoJ and for patiently tolerating its (and my) various shortcomings.
Whereas no direct grant funding went into the development of MorphoJ, the early development of the software was stimulated and aided in one way or another by research in my lab has come from the following organizations:
This section outlines the licence and copyright conditions for the MorphoJ software (in the form of either the MorphoJ.jar or MorphoJ.exe files, which are part of the MorphoJ distribution) and the external libraries that are included in the MorphoJ distributions.
Copyright 2008-2023 Christian Peter Klingenberg.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
The Java 17 OpenJDK implementation used to prepare MorphoJ from
release 1.08 onward is Eclipse Temurin.
Packages cern.colt* , cern.jet*, cern.clhep
Copyright (c) 1999 CERN - European Organization for Nuclear Research.
Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty.
Copyright 1999-2021 The Apache Software Foundation
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Redistribution and use of this software and associated documentation ("Software"), with or without modification, are permitted provided that the following conditions are met:
THIS SOFTWARE IS PROVIDED BY METASTUFF, LTD. AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESSED 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 METASTUFF, LTD. OR ITS 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.
Copyright 2001-2005 (C) MetaStuff, Ltd. All Rights Reserved.
Copyright 2008-2023 Christian Peter Klingenberg.