The current state of ImageJ

Currently, ImageJ has been cited in more than 200 publications since the beginning of 2015, in fields ranging from physics and engineering to medicine and biology. Many publications are about newly developed plugins that were specifically developed to solve a problem within a certain subfield of science. On the ImageJ website, the page that lists plugins has more than 1000 plugins available. A few research institutes even have collections of multiple plugins available that were developed there as research projects. Most, if not all, are open source plugins with the full source code available. You can adjust and customize the code to suit your needs.

ImageJ2

ImageJ is still under active development, and new features and bug fixes are added to the core distribution on a regular basis. Currently, the development of a revised system for ImageJ is being developed. It is called ImageJ2. The goals of ImageJ2 are to better support multidimensional data as well as create a more extensible platform that can be used as a library instead of a standalone application. It will also create a more consistent environment for development and extension. One of the features being developed is the updating mechanism for ImageJ. Currently, it is possible to update ImageJ automatically using a central repository, and one of the goals of ImageJ2 is to expand this option to plugins and other features and allow tracking of bugs and features. However, one of the core requirements in the new ImageJ2 system is backward compatibility. This goal means that plugins developed now will stay functional in future releases of ImageJ. The current status is indicated as beta, which means the plugin is functional but may still contain bugs and is not optimized for performance yet.

SciFIO and OME-XML

Other developments related to image are those related to image formats and standards. Currently, all major commercial acquisition platforms store image data in unique proprietary file formats. The SCIFIO project is aimed at creating an extensible and integrated interface to handle images of different formats. It will support more image formats and allow for additional options to be set when importing the data, such as autoscaling, loading metadata, and loading the data in different ImageJ image types. However, it is still under active development, and some of the features do not quite work in a production environment (yet).

The OME-XML (Open Microscopy Environment-XML) project is aimed at creating a file format that contains all the image and metadata in a standardized format. This would facilitate the exchange of microscope image data, regardless of the equipment used for acquisition. It is mainly focused on the exchange of microscopy data in the field of life sciences. It contains all the experimental and setup data as well as the pixel data in a single file specification.

Bio-formats

Besides the OME-XML format, which is focused on integrating acquisition and processing across multiple acquisition platforms, there is also active development of the plugin used to import many image formats currently in existence. This plugin, called Bio-Formats, is mostly focused on image formats from the life sciences. However, it also supports FITS data, which is used in the field of astronomy and space exploration. It currently supports (to different degrees) 140 different image formats and converts them to the OME-XML format for use in ImageJ.