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.
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.
ImageJ 1.x format handling
With the original ImageJ, 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
HandleExtraFileTypesinstalled 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
HandleExtraFileTypeson 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 ImageJ’s built in support for certain file formats. In particular, ImageJ supports only a subset of the TIFF specification, and this issue cannot be circumvented via