ome-xml.jar, scifio.jar, loci-common.jar
Bioformats libraries needed for writing OME Tiffs
Downloaded: 9/2012
http://loci.wisc.edu/bio-formats/downloads

slf4j-api-1.7.1.jar
3rd party logging utility used by Bioformats; needed by Bioformats jars which are needed to write OME Tiffs
Version 1.7.1
Downloaded: 9/21/2012
http://www.slf4j.org/download.html

AbsoluteLayout.jar
Classes needed by some GUIs designed in the Netbeans GUI builder.  Inclusion of this file may need to be evaluated from time to time.

TSFProto.jar
Classes needed to read and write Gaussian fitting data in the Tagged Spot Format. This is to stre single molecule data such as in STORM/PALM imaging.  It uses Google Protocol Buffers under the hood.

gproto.jar
Compiled version of Google Protocol Buffers (https://developers.google.com/protocol-buffers/).

bsh-2.04b.jar
Beanshell interpreter and environment

ij.jar
ImageJA (source: https://github.com/imagej/ImageJA)
JAR from Maven Central (net.imagej/ij; http://search.maven.org/#browse%7C-1544119488)
JAR renamed to ij.jar
(Note: ImageJA is an ImageJ1 source tree maintained by the ImageJ2 team; it
tracks ImageJ1 versions but clarifies the exact correspondence between source
code and binary release versions.)

jfreechart-1.0.13.jar
Library used for plotting data (http://www.jfree.org/jfreechart/).

lwm.jar
Clojure implementation of local weighted maxima algorithm.  No longer needed as there is now Java code to do the same.

rsyntaxtextarea.jar
RSyntaxArea is a syntax highlighting text editor component. Information: http://fifesoft.com/rsyntaxtextarea/. Source: https://github.com/bobbylight/RSyntaxTextArea. License: Modified BSD: https://github.com/bobbylight/RSyntaxTextArea/blob/master/distfiles/RSyntaxTextArea.License.txt.  Source code was pulled from Github on 04/19/2014 and compiled using the command: "ant".  

guava-17.0.jar
Google's core libraries, which we currently only need for EventBus.

commons-math3-3.2.jar
Apache Commons Math 3 (packages do not conflict with commons-math 2.x).
From http://archive.apache.org/dist/commons/math/binaries/commons-math3-3.2-bin.zip