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This page describes the core SciJava software libraries.

SciJava

SciJava is a collaboration of projects providing software for scientific computing—an effort to cooperate and reuse code when feasible.

It is also a collection of foundational software libraries, upon which ImageJ2 and Fiji are built.

The SciJava component collection

The following component layers are part of the SciJava component collection:

  • SciJava - foundational layer unspecific to image processing, including the SciJava Common shared library with powerful plugin framework and application container, and plugins built on it.
  • ImgLib2 - core libraries for N-dimensional image processing.
  • SCIFIO - core libraries for N-dimensional image I/O.
  • ImageJ2 - core libraries and application for N-dimensional image processing.
  • Fiji - “batteries-included” distribution of ImageJ and ImageJ2, bundling a lot of plugins which facilitate scientific image analysis.
  • BigDataViewer - re-slicing browser and Fiji plugin for terabyte-sized multi-view image sequences
  • TrakEM2 - Fiji plugin suite for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation.
  • Bio-Formats - libraries and ImageJ plugins for life sciences image format I/O.

All components in this collection are managed by SciJava’s Bill of Materials to make it easier for downstream components to use them without version conflicts.

The SciJava pledge

The following projects are part of the SciJava pledge to work together, reuse code and synergize wherever possible:

ImageJ2

Fiji

Micro-Manager

VCell

Alida

MiToBo

See the Architecture and Governance pages, as well as the SciJava website, for further details.

SciJava Common

SciJava Common is a common library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ2 and SCIFIO.

Plugin framework

First and foremost, SciJava Common is a plugin framework—a base for developing highly modular and extensible Java applications.

Plugin discovery

All plugins available on Java’s classpath are automatically discovered and made available. This is accomplished by scanning classpath resources for the file path META-INF/json/org.scijava.plugin.Plugin. Such files are generated at compile time by a Java annotation processor that writes them in response to @Plugin annotations on Java classes, an idea inspired by the SezPoz project.

Application container

All program state, such as available plugins, is accessible from a root object known as the application context.

Services

Whereas ImageJ is a singleton, with static methods to access much of its functionality, ImageJ2 encapsulates its program state in the application context, allowing multiple simultaneous such contexts in the same JVM.

ImageJ2 encapsulates its various parts as separate “services” that provide related state functionality and track related program state. An instance of the net.imagej.ImageJ class is nothing more than a collection of these services; this instance is referred to as the “application gateway.” Services are defined as interfaces, with concrete implementations as plugins. This design provides seams in the right places so that behavior at every level can be customized and overridden.

SciJava services

Here are a few of SciJava Common’s major core services:

  • AppService - Tracks software applications (SCIFIO, ImageJ2, etc.) present in the context.
  • DisplayService - Tracks available displays, as well as the active display, and provides the means to create new displays to visualize data.
  • EventService - Publishes events to the event bus, and allows interested parties to subscribe to them. The service provides the central means of communication between various parts of the codebase.
  • IOService - General tools for opening and saving data within the context.
  • MenuService - Builds the application menu structure.
  • ModuleService - Tracks available modules, and provides the infrastructure for executing them.
  • ObjectService - Tracks available objects of various types, including Datasets and Displays.
  • OptionsService - Tools for managing program settings.
  • PlatformService - Provides hooks for extending the application’s behavior depending on the deployment platform (operating system, version of Java, etc.).
  • PluginService - Tracks available plugins, and provides the infrastructure for executing them (using the ModuleService).
  • ScriptService - Provides utilities for running scripts and macros.
  • StatusService - Publishes status updates for ongoing operations.
  • ThreadService - Manages multithreading.
  • ToolService - Tracks available tools—logic binding user input to behavior—as well as the active tool (selected on the toolbar).
  • UIService - Discovers and launches a user interface for interacting with ImageJ.

ImageJ2 services

Some of the services which ImageJ2 adds:

SCIFIO services

SCIFIO provides several additional services—in particular:

The SciJava menuing system is divided into several layers, to make it easier to override its behavior or customize its appearance in a user interface.

Modules

Each module known to the system (via the ModuleService can have a menuPath that says where it should live (by default) in the menu. It also has a menuRoot that says in which menu it should live, with the default being the APPLICATION_MENU_ROOT, indicating the main application menu structure.

The MenuService takes care of constructing ShadowMenu tree structures for all available modules in the system, using their menuPath and menuRoot values. These tree structures are UI-agnostic. There is one ShadowMenu per menuRoot, which can be requested at will from the MenuService.

User interfaces

The UIService then takes care of constructing an actual UI-specific menu bar (or whatever UI components and/or widgets it wants) from the available ShadowMenus. There is a type hierarchy beneath the MenuCreator interface intended for this purpose; for example, the SwingJMenuBarCreator implements MenuCreator to create and maintain a Swing JMenuBar that reflects the state of a particular ShadowMenu.

How changes propagate

When modules are added, removed or changed (via ModulesAddedEvent, ModulesRemovedEvent, ModulesUpdatedEvent), the MenuService listens and updates the associated ShadowMenu(s) accordingly. It notifies interested parties that it has done so by firing a corresponding event: MenusAddedEvent, MenusRemovedEvent, or MenusUpdatedEvent.

API Version History

A history of API changes is available at: https://abi-laboratory.pro/java/tracker/timeline/scijava-common/

Further reading