Features: Difference between revisions

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__NOTOC__
__NOTOC__
The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop<br/>
Alida provides a framework for easy development and usage of data analysis procedures.<br/>
new plugins and algorithms in the field of custom image analysis and processing, and those who want to use<br/>
Below an overview of its main features is given.<br/><br/>
custom plugins from [http://rsbweb.nih.gov/ij/ ImageJ] in their daily research.<br/><br/>


A list of contained features and their description in short detail can be found below.<br/><br/>
'''Operator Concept'''<br/>
* common interface for all implemented operators: unified access to all operator parameters, standardized operator invocation procedures
* various parameter types: input, output and combined input/output parameters
* support for operator class inheritance and operators as parameters
* dynamic addition and removal of parameters at runtime
* callback functions attached to parameters and invoked in case of parameter value changes
* support for ''controllable operators'' which can be paused/continued and stopped by the user
* extensible provider framework for data type I/O with built-in support for native data types, enumerations, collections, ...
* simple definition of new user-defined I/O data types by ''parameterized classes''<br/><br/>


'''Operators'''<br/>
'''Automatic Process Documentation'''<br/>
The operator concept is one of the major features in MiToBo. By developing such operators, the processing steps<br/>
* inherent ''self-documentation'' of all calls to operators, i.e. of entire analysis procedures
can be linked to a directed graph structure, which allows '''self-documentation''' of the entire image analysis process.<br/>
* each result data object accompanied by individual ''history graph'' in XML format
Each resulting data object, being the result of a certain operator or sequence of operations, is associated with a<br/>
* history graph exploration tool ''Chipory'', a comfortable graph visualization tool for exploring graph data structures based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however, extended to meet the special requirements of Alida's history graphs.<br/><br/>
'''history graph''' in XML format.<br/><br/>


'''Plugins'''<br/>
'''User Interfaces'''<br>
The well known and very powerful plugin concept of [http://rsbweb.nih.gov/ij/ ImageJ] is also available in MiToBo.<br/>
* automatic generation of user interfaces for command line and graphical applications
Every user and developer, using MiTobo, can easily create new plugins and customize existing [http://rsbweb.nih.gov/ij/plugins/index.html ImageJ plugins],<br/>
* flexible command line parser supporting regular expressions and various I/O channels (file, console)
to use the automatic documentation of the plugin via the operator concept of MiToBo for instance.<br/><br/>
* handy configuration and control windows for configuring and running operators in graphical environments
* support for saving/loading operator configuration parameters in XML format
* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/>


'''Data types'''<br/>
'''Grappa - The Graphical Workflow Editor'''<br>
MiToBo defines a set of its own data types. For example, a new image data type was developed to improve the<br/>
* graphical combination of operator nodes into workflows
[http://rsbweb.nih.gov/ij/ ImageJ] image classes.<br/><br/>
* built-in compatibility checks on dragging edges
 
* provider framework for automatic data type conversions
'''Applications'''<br/>
* user-friendly visual feedback about node states (unconfigured, ready to run, terminated, etc.)
Using the plugin and operator concept combined with the large amount of already implemented datatypes and operators,<br/>
* different workflow execution modes (complete workflows, sub-workflows, individual nodes)
a huge coupple of applications on biological and biomedical images can be developed.<br/><br/>

Latest revision as of 18:23, 10 March 2016

Alida provides a framework for easy development and usage of data analysis procedures.
Below an overview of its main features is given.

Operator Concept

  • common interface for all implemented operators: unified access to all operator parameters, standardized operator invocation procedures
  • various parameter types: input, output and combined input/output parameters
  • support for operator class inheritance and operators as parameters
  • dynamic addition and removal of parameters at runtime
  • callback functions attached to parameters and invoked in case of parameter value changes
  • support for controllable operators which can be paused/continued and stopped by the user
  • extensible provider framework for data type I/O with built-in support for native data types, enumerations, collections, ...
  • simple definition of new user-defined I/O data types by parameterized classes

Automatic Process Documentation

  • inherent self-documentation of all calls to operators, i.e. of entire analysis procedures
  • each result data object accompanied by individual history graph in XML format
  • history graph exploration tool Chipory, a comfortable graph visualization tool for exploring graph data structures based on Chisio, however, extended to meet the special requirements of Alida's history graphs.

User Interfaces

  • automatic generation of user interfaces for command line and graphical applications
  • flexible command line parser supporting regular expressions and various I/O channels (file, console)
  • handy configuration and control windows for configuring and running operators in graphical environments
  • support for saving/loading operator configuration parameters in XML format
  • batch mode option in GUIs to apply operators to sets of input data objects

Grappa - The Graphical Workflow Editor

  • graphical combination of operator nodes into workflows
  • built-in compatibility checks on dragging edges
  • provider framework for automatic data type conversions
  • user-friendly visual feedback about node states (unconfigured, ready to run, terminated, etc.)
  • different workflow execution modes (complete workflows, sub-workflows, individual nodes)
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