FigureComposer is a standalone Java application for preparing, revising and reviewing detailed scientific figures intended for journal publication. It is a mature application that has been used by members of Stephen G. Lisberger's laboratory at Duke University since 2007, as well as some others in the neuroscience commmunity.
NOTE: I am no longer actively developing FC. I have made this repo available for anyone in the neuroscience community that continues to use the application and might wish to fork the repo to adapt the program for their own use.
An online user's guide provides a thorough introduction to the program, a detailed format description of the application's figure document format (FypML), a complete version history, and a downloads page where you can get the latest release.
An (unsigned) application bundle is available for installation on MacOS, an installer EXE for Windows, and an executable JAR for Linux. You must separately install a Java Runtime Environment compatible with your host operating system in order to run FigureComposer. As of version 5.2.0, a Java 8 runtime is required. For details, see the online guide.
NOTE: As of version 5.5.0, the code base is JDK11-compliant, and a Java 11 runtime is required. Recommend using Amazon Corretto 11.
Researchers in the Lisberger and other labs have used Matlab
extensively over the years to process their experimental data and prepare draft figures for journal publication. I have
written a number of Matlab scripts to address the issue of how to conveniently get data into or out of a FigureComposer
figure (FypML file). You will find these scripts in the supporting folder within the repo. These are probably of
limited use, since FigureComposer (as of version 4.2.3) can import many Matlab figure (*.fig) files directly.
The various utility scripts are described in details in the online guide.
The matfig2fyp() script relies on JAR files hhmi-ms-common.jar and hhmi-ms-datanav.jar, which are included in the
Figure Composer download ZIP and must be installed in Matlab's Java class path. As of version 5.5.0, the
class files in these JARs are JDK11-compliant, so they require that Matlab be configured to use a Java 11 runtime.
Matlab's default bundled JRE is still Java 8 as of R2024a, but it supports using OpenJDK 11 runtimes such as Amazon
Corretto 11. To specify the JRE that Matlab should use, run jenv(<jre_home>) from the Matlab command line (where
<jre_home> is the installation path for the OpenJDK 11-compliant runtime environment), then restart Matlab.
- The code base in this repository is set-up as an IntelliJ IDEA project, and the IDEA project settings are included in the repo.
- The
macosxdistfolder contains resource files for packaging FC as a MacOS application bundle, which is then archived in a ZIP file for distribution. - The
windistfolder contains resource files for building a Windows installer EXE for FC. The installer is created on a Windows workstation using InnoSetup. - An Ant build file,
release.xml, semi-automates the build process: creating the source JARs for the three modules in the IDEA project (common,jmatio, andfigurecomposer), packaging the class files in module JARS, and preparing ZIP archives for installing FC on MacOS, Windows, and Linux. Be sure to read through this file carefully before attempting to build your own release, and always rebuild the entire project before running the Ant build.
Figure Composer was created by Scott Ruffner. It is licensed under the terms of the MIT license.
FigureComposer was developed with funding provided by the Stephen G. Lisberger laboratory in the Department of Neurobiology at Duke University.
As a full-featured Java Swing application, it relies heavily upon Oracle's Java Development Kit; as of June 2024, it is JDK11-compliant and built with Amazon Corretto 11.
In addition, it makes use of a number of open-source software packages. Without these third-party packages, FigureComposer would have been a much more difficult endeavor.
- FypML figure documents have been read and written using MXP1, an open-source implementation of an XML pull parser. As of version 5.2.0, this library is no longer used; instead, FC relies on the Streaming API for XML Processing that is now part of the Java runtime environment.
- The JavaScript Object Notation (JSON) data interchange format is used heavily, and the application relies on the org.json package to read and write JSON data.
- Matlab FIG files are read and parsed using a modified version of the Java MAT-file IO (JMatIO) package.
- FypML figures are exported to Portable Document Format (PDF) and Scalable Vector Graphics (SVG) files with the help of the iText5 PDF and the JFreeSVG libraries, respectively.