To use Bio-Formats with your Java Web Start application, we recommend using bio-formats.jar rather than loci_tools.jar—the latter is merely a bundle of bio-formats.jar plus all its optional dependencies.

The loci_tools.jar bundle is intended as a convenience (e.g., to simplify installation as an ImageJ plugin), but is by no means the only solution for developers. We recommend using bio-formats.jar as a separate entity depending on your needs as a developer.

The bundle is quite large because we have added support for several formats that need large helper libraries (e.g., Imaris's HDF-based format). However, these additional libraries are optional—Bio-Formats has been coded using reflection so that it can both compile and run without them.

When deploying a JNLP-based application, using loci_tools.jar directly is not the best approach, since every time Bio-Formats is updated, the server would need to feed another 8+ MB JAR file to the client. Rather, Web Start is a case where you should keep the JARs separate, since JNLP was designed to make management of JAR dependencies trivial for the end user. By keeping bio-formats.jar and the optional dependencies separate, only a <1 MB JAR needs to be updated when bio-formats.jar changes.

As a developer, you have the option of packaging bio-formats.jar with as many or as few optional libraries as you wish, to cut down on file size as needed. You are free to make whatever kind of "stripped down" version you require. You could even build a custom bio-formats.jar that excludes certain classes, if you like.

For an explicit enumeration of all the optional libraries included in loci_tools.jar, see the loci-tools.libraries variable of the build.properties file of the distribution. You can also read our notes about each in the source distribution's Ant build.xml script.