Features - Revision history

Moeller at 17:23, 10 March 2016

2016-03-10T17:23:37Z

← Older revision		Revision as of 19:23, 10 March 2016
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	* automatic generation of user interfaces for command line and graphical applications		* 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)		* flexible command line parser supporting regular expressions and various I/O channels (file, console)
	* handy configuration and control windows for graphical ~~user interfaces~~		* handy configuration and control windows for configuring and running operators in graphical environments
	* support for saving/loading operator configuration parameters in XML format		* 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/>		* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/>

Moeller at 17:22, 10 March 2016

2016-03-10T17:22:48Z

← Older revision		Revision as of 19:22, 10 March 2016
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	* inherent ''self-documentation'' of all calls to operators, i.e. of entire analysis procedures		* 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		* each result data object accompanied by individual ''history graph'' in XML format
	* history graph exploration tool~~: '~~''Chipory''~~'<br/>Chipory is~~ a comfortable graph visualization tool for exploring graph data structures~~. It is~~ based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however,~~<br/>~~extended to meet the special requirements of Alida's history graphs.<br/><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/>

	'''User Interfaces'''<br>		'''User Interfaces'''<br>

Moeller at 17:22, 10 March 2016

2016-03-10T17:22:03Z

← Older revision		Revision as of 19:22, 10 March 2016
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	'''Automatic Process Documentation'''<br/>		'''Automatic Process Documentation'''<br/>
	* inherent '''self-documentation''' of all calls to operators, i.e. of entire analysis procedures		* inherent ''self-documentation'' of all calls to operators, i.e. of entire analysis procedures
	* result data ~~objects~~ accompanied by individual '''history ~~graphs'~~'' in XML format		* each result data object accompanied by individual ''history graph'' in XML format
	* history graph exploration tool: '''Chipory'''<br/>Chipory is a comfortable graph visualization tool for exploring graph data structures. It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however,<br/>extended to meet the special requirements of Alida's history graphs.<br/><br/>		* history graph exploration tool: '''Chipory'''<br/>Chipory is a comfortable graph visualization tool for exploring graph data structures. It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however,<br/>extended to meet the special requirements of Alida's history graphs.<br/><br/>

Moeller at 17:19, 10 March 2016

2016-03-10T17:19:40Z

← Older revision		Revision as of 19:19, 10 March 2016
Line 22:		Line 22:
	* flexible command line parser supporting regular expressions and various I/O channels (file, console)		* flexible command line parser supporting regular expressions and various I/O channels (file, console)
	* handy configuration and control windows for graphical user interfaces		* handy configuration and control windows for graphical user interfaces
	* support for saving/loading ~~operators~~ configuration parameters in XML format		* 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/>		* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/>

Moeller at 17:19, 10 March 2016

2016-03-10T17:19:13Z

← Older revision		Revision as of 19:19, 10 March 2016
Line 11:		Line 11:
	* support for ''controllable operators'' which can be paused/continued and stopped by the user		* 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, ...		* 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''		* simple definition of new user-defined I/O data types by ''parameterized classes''<br/><br/>
	<br/><br/>

	'''Automatic Process Documentation'''<br/>		'''Automatic Process Documentation'''<br/>
Line 24:		Line 23:
	* handy configuration and control windows for graphical user interfaces		* handy configuration and control windows for graphical user interfaces
	* support for saving/loading operators configuration parameters in XML format		* support for saving/loading operators configuration parameters in XML format
	* batch mode option in GUIs to apply operators to sets of input data objects		* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/>
	<br/><br/>

	'''Grappa - The Graphical Workflow Editor'''<br>		'''Grappa - The Graphical Workflow Editor'''<br>

Moeller at 17:18, 10 March 2016

2016-03-10T17:18:29Z

← Older revision		Revision as of 19:18, 10 March 2016
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	__NOTOC__		__NOTOC__
	Alida provides a framework for easy development and usage of data analysis procedures.<br/><br/>		Alida provides a framework for easy development and usage of data analysis procedures.<br/>
			Below an overview of its main features is given.<br/><br/>

	'''~~Operators~~'''<br/>		'''Operator Concept'''<br/>
	~~The operator concept is the main ingredient of Alida. It defines a~~ common interface for all operators ~~by which their~~ input and output parameters can be ~~accessed~~,~~<br> and which also defines a standardized operator invocation procedure. Moreover~~, ~~different processing steps of an analysis procedure~~, i.e. ~~different operator calls,~~<br> ~~can be linked to a directed graph structure, which allows~~ '''self-documentation''' of ~~the~~ entire analysis ~~process.<br>~~		* common interface for all implemented operators: unified access to all operator parameters, standardized operator invocation procedures
	~~Each resulting~~ data ~~object in Alida, being the result of a certain operator or sequence of operations, is associated with a~~ '''history ~~graph~~''' in XML format ~~documenting its origins and manipulative actions having been performed~~ on it.<br/><br/>		* 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/>

			'''Automatic Process Documentation'''<br/>
			* inherent '''self-documentation''' of all calls to operators, i.e. of entire analysis procedures
			* result data objects accompanied by individual '''history graphs''' in XML format
			* history graph exploration tool: '''Chipory'''<br/>Chipory is a comfortable graph visualization tool for exploring graph data structures. It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however,<br/>extended to meet the special requirements of Alida's history graphs.<br/><br/>

	'''User Interfaces'''<br>		'''User Interfaces'''<br>
	~~The clearly defined operator interface and the unified invocation mechanism allows for generic execution~~ of ~~operators based on Alida.<br>~~		* automatic generation of user interfaces for command line and graphical applications
	~~In particular, generic~~ user interfaces, ~~like GUIs or commandline interfaces, can be generated in a fully automatic way~~ and ~~are well-suited~~ for ~~interaction<br> with arbitrary operators. Alida already includes~~ user interfaces for ~~graphical interaction based on Swing and for executing~~ operators ~~from commandline.<br/><br/>~~		* flexible command line parser supporting regular expressions and various I/O channels (file, console)
			* handy configuration and control windows for graphical user interfaces
	~~'''History Graphs'''<br/>~~		* support for saving/loading operators configuration parameters in XML format
	~~Analysis procedures inherently define an acyclic directed graph data structure which Alida make explicit~~ in ~~terms of<br/>~~		* batch mode option in GUIs to apply operators to sets of input data objects
	~~history graphs. They define visual representations~~ of data ~~analysis procedures subsuming operators, their order of<br/>~~		<br/><br/>
	~~invocation and their parameters. The graphs allow for easy archival and later reconstruction of analysis procedure and<br/>~~
	~~can be visualized in a comfortable manor with '''Chipory'''.~~<br/><br/>

	'''~~Chipory~~'''<br/>		'''Grappa - The Graphical Workflow Editor'''<br>
	~~Chipory is a comfortable graph visualization tool~~ for ~~exploring graph~~ data ~~structures~~. ~~It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio]~~, ~~however~~,~~<br/>~~		* graphical combination of operator nodes into workflows
	~~extended to meet the special requirements of Alida's history graphs.<br/><br/>~~		* 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)

Sysop at 16:41, 1 March 2012

2012-03-01T16:41:30Z

← Older revision		Revision as of 18:41, 1 March 2012
Line 1:		Line 1:
	__NOTOC__		__NOTOC__
	Alida provides a framework for ~~automatic documentation~~ of data analysis procedures.<br/><br/>		Alida provides a framework for easy development and usage of data analysis procedures.<br/><br/>

	'''Operators'''<br/>		'''Operators'''<br/>
	The operator concept is the main ingredient of Alida. ~~By developing such~~ operators, ~~the processing steps~~<br/>		The operator concept is the main ingredient of Alida. It defines a common interface for all operators by which their input and output parameters can be accessed,<br> and which also defines a standardized operator invocation procedure. Moreover, different processing steps of an analysis procedure, i.e. different operator calls,<br> can be linked to a directed graph structure, which allows '''self-documentation''' of the entire analysis process.<br>
	of an analysis procedure can be linked to a directed graph structure, which allows '''self-documentation'''~~<br/>~~		Each resulting data object in Alida, being the result of a certain operator or sequence of operations, is associated with a '''history graph''' in XML format documenting its origins and manipulative actions having been performed on it.<br/><br/>
	of the entire analysis process. Each resulting data object, being the result of a certain operator or sequence ~~<br/>~~
	of operations, is associated with a '''history graph''' in XML format.<br/><br/>		'''User Interfaces'''<br>
			The clearly defined operator interface and the unified invocation mechanism allows for generic execution of operators based on Alida.<br>
			In particular, generic user interfaces, like GUIs or commandline interfaces, can be generated in a fully automatic way and are well-suited for interaction<br> with arbitrary operators. Alida already includes user interfaces for graphical interaction based on Swing and for executing operators from commandline.<br/><br/>

	'''History Graphs'''<br/>		'''History Graphs'''<br/>

Sysop at 07:50, 27 April 2011

2011-04-27T07:50:34Z

← Older revision		Revision as of 09:50, 27 April 2011
Line 5:		Line 5:
	The operator concept is the main ingredient of Alida. By developing such operators, the processing steps<br/>		The operator concept is the main ingredient of Alida. By developing such operators, the processing steps<br/>
	of an analysis procedure can be linked to a directed graph structure, which allows '''self-documentation'''<br/>		of an analysis procedure can be linked to a directed graph structure, which allows '''self-documentation'''<br/>
	of the entire analysis process.~~<br/>~~		of the entire analysis process. Each resulting data object, being the result of a certain operator or sequence <br/>
	Each resulting data object, being the result of a certain operator or sequence of operations, is associated with a<br/>		of operations, is associated with a '''history graph''' in XML format.<br/><br/>
	'''history ~~graph~~''' ~~in XML format~~.<br/><br/>
			'''History Graphs'''<br/>
			Analysis procedures inherently define an acyclic directed graph data structure which Alida make explicit in terms of<br/>
			history graphs. They define visual representations of data analysis procedures subsuming operators, their order of<br/>
			invocation and their parameters. The graphs allow for easy archival and later reconstruction of analysis procedure and<br/>
			can be visualized in a comfortable manor with '''Chipory'''.<br/><br/>

			'''Chipory'''<br/>
			Chipory is a comfortable graph visualization tool for exploring graph data structures. It is based on [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio], however,<br/>
			extended to meet the special requirements of Alida's history graphs.<br/><br/>

Sysop at 07:44, 27 April 2011

2011-04-27T07:44:15Z

@@ Line 1: / Line 1: @@
 __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 automatic documentation of data analysis procedures.<br/><br/>
 '''Operators'''<br/>
-The operator concept is one of the major features in MiToBo. By developing such operators, the processing steps<br/>
+The operator concept is the main ingredient of Alida. By developing such operators, the processing steps<br/>
-can be linked to a directed graph structure, which allows '''self-documentation''' of the entire image analysis process.<br/>
+of an analysis procedure can be linked to a directed graph structure, which allows '''self-documentation'''<br/>
 Each resulting data object, being the result of a certain operator or sequence of operations, is associated with a<br/>
 '''history graph''' in XML format.<br/><br/>

Sysop: Created page with "NOTOC The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop
new plugins and algorithms in the field of custom im..."

2011-04-27T07:42:21Z

Created page with "__NOTOC__ The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop new plugins and algorithms in the field of custom im..."

New page

__NOTOC__
The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop 
new plugins and algorithms in the field of custom image analysis and processing, and those who want to use 
custom plugins from [http://rsbweb.nih.gov/ij/ ImageJ] in their daily research. 

A list of contained features and their description in short detail can be found below. 

'''Operators''' 
The operator concept is one of the major features in MiToBo. By developing such operators, the processing steps 
can be linked to a directed graph structure, which allows '''self-documentation''' of the entire image analysis process. 
Each resulting data object, being the result of a certain operator or sequence of operations, is associated with a 
'''history graph''' in XML format. 

'''Plugins''' 
The well known and very powerful plugin concept of [http://rsbweb.nih.gov/ij/ ImageJ] is also available in MiToBo. 
Every user and developer, using MiTobo, can easily create new plugins and customize existing [http://rsbweb.nih.gov/ij/plugins/index.html ImageJ plugins], 
to use the automatic documentation of the plugin via the operator concept of MiToBo for instance. 

'''Data types''' 
MiToBo defines a set of its own data types. For example, a new image data type was developed to improve the 
[http://rsbweb.nih.gov/ij/ ImageJ] image classes. 

'''Applications''' 
Using the plugin and operator concept combined with the large amount of already implemented datatypes and operators, 
a huge coupple of applications on biological and biomedical images can be developed.

Features - Revision history

Moeller at 17:23, 10 March 2016

Moeller at 17:22, 10 March 2016

Moeller at 17:22, 10 March 2016

Moeller at 17:19, 10 March 2016

Moeller at 17:19, 10 March 2016

Moeller at 17:18, 10 March 2016

Sysop at 16:41, 1 March 2012

Sysop at 07:50, 27 April 2011

Sysop at 07:44, 27 April 2011

Sysop: Created page with "__NOTOC__ The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop new plugins and algorithms in the field of custom im..."

Sysop: Created page with "NOTOC The Microscope Image Analysis Toolbox MiToBo contains a lot of new features for scientist, who want to develop
new plugins and algorithms in the field of custom im..."