ImageJ

Development
Topics Overview Philosophy Architecture Source code Project management Coding style Debugging
Tools GitHub Git Maven IDEs Travis AppVeyor Dotfiles
Guides Writing plugins ImageJ Ops Contributing to a plugin Distributing your plugins Development lifecycle Building a POM Developing with Eclipse Hands-on debugging Adding new ops Adding new formats Using native libraries Tips for developers Tips for C++ developers ImageJ 1.x plugins Versioning Logging Uber-JARs

Before an image can be analyzed, it needs to be opened properly. The way scientific image data can be stored varies wildly - with custom formats as numerous as the different brands and models of instruments used in their acquisition. Therefore, supporting a wide variety of formats is critical to the success of an image analysis platform like ImageJ.

With ImageJ 1.x, a special HandleExtraFileTypes plugin exists that can be modified to support new data formats—but it has some significant disadvantages:

• It only provides limited extensibility: there can only be one HandleExtraFileTypes installed into ImageJ at a time, so all desired modifications to the plugin must be somehow combined. This makes it impossible to, for example, ship a different HandleExtraFileTypes on two different ImageJ Update Sites and have both additions be available in the same installation.
• Data formats added in this manner cannot override or extend ImageJ1's built in support for certain file formats. In particular, ImageJ1 supports only a subset of the TIFF specification, and this issue cannot be circumvented via HandleExtraFileTypes modifications.

ImageJ2 provides a comprehensive solution to the issue of data formats in the form of SCIFIO data format plugins. SCIFIO, the SCientific Image Format Input and Output library, is a flexible framework for image format support. To get started writing SCIFIO formats:

• Check out the SCIFIO tutorials.
• Look at simple existing formats for a starting point.

See also

• Bio-Formats