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__NOTOC__
== Quick Start ==
== Requirements ==
The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:
MiToBo requires Java 1.6 or later.  
 
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br>
 
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].
 
<br>
For installing MiToBo this way you need to activate the following site:
* MiToBo
For some operators additional sites are required:
* Biomedgroup (e.g., for PaCeQuant)
 
<br>
More details how to install and run MiToBo can be found on our [[Installation]] page.
<br>
 
== Downloads and Releases ==
 
The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.
 
Since release 1.3 we support Maven for managing MiToBo's resources.<br> You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:
 
[https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo]
 
There are two MiToBo distributions available:
* <b>MiToBo:</b><br> this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;<br> <b>not included</b> are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes<br>
* <b>MiToBo-Plugins:</b><br> this package contains the complete MiToBo distribution, some special plugins like the [[Applications/MTBCellCounter | MTB Cell Counter]], and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ<br>
 
Since release 1.8 MiToBo's implementation requires at least Java 1.8.
<br>
 
At the bottom of this page additional files are available for download:
* Old distributions: complete distributions including all dependencies, scripts, documentation, etc.
* Binaries only: only the jar archives, no dependencies neither documentation
* APIs: Javadoc APIs
<br>
 
== Maven Project Template ==
Using MiToBo as a library for own developments can best be done by making use of Maven.<br>
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.
 
For getting started with MiToBo and Maven a project template is provided:
 
[http://www.informatik.uni-halle.de/mitobo/downloads/maven/mitobo-demo-project-1.2-src.zip Maven project template [zip]]
 
The project is readily configured and you can immediately start with own developments.<br>
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.
 
Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.<br>
You can check the Java version by running 'mvn --version' from command line.<br>
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.
 
You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.<br>
The zip file contains a README file containing more information about installing and configuring the project template.
<br/>


The following external jars are needed to run MiToBo plugins and use the code:


* [http://rsbweb.nih.gov/ij/ ImageJ], Version 1.44
== Manual ==
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
 
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.2.2
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)


For using explicite active contours (snakes) in MiToBo, additionally the following library is required:
* MiToBo-Guide, Version 1.0 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]
<br>


* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2
== Additional resources ==


MiToBo also relies on some libraries provided by the MiToBo project itself.<br>
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
For using snakes in particular native C++ libraries are required.<br>
<br/>
If you download the MiToBo binaries you will find all of them included in the zip file.<br/>
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.
A list of all project libraries required can be found at the bottom of this page.<br/>


== Current release (v0.9.6)==
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR>
* MiToBo Binaries [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-0.9.6.zip zip] (includes MiToBo binaries, license information and additional jars provided by the MiToBo project)
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR>
* MiToBo Sources [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-0.9.6.zip zip] (includes only the MiToBo sources)
* For Windows with 32-bit architecture a self extracting installer  including an executable of Chipory is available.
* MiToBo API [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-0.9.6.zip zip]
<br/>
<br/>
Download the current release:
* Chipory binary  [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
<br>
== Logo ==
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]
== Earlier releases of MiToBo (< 1.5) ==


== All versions of MiToBo ==
Since release 1.3 MiToBo's resources are available from our Maven archive server: [https://moon.informatik.uni-halle.de/archiva/]<br>Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.<br> All other releases can be accessed via the list below.<br>


{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"
Line 35: Line 96:
! API  
! API  
! Date
! Date
|-
| 1.4.3
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-bin.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3.jar jar]
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.3-javadoc.jar jar]
| March 31st, 2015 (Support for callbacks)
|-
| 1.4.2
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-bin.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2.jar jar]
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.2-javadoc.jar jar]
| Jan 7th, 2015
|-
| 1.4.1
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-bin.zip zip]
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1.jar jar]
| [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/mitobo-1.4.1-javadoc.jar jar]
| Dec 1st, 2014
|-
| 1.2
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.2.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.2.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.2.zip zip]
| May 17th, 2013
|-
|-
| 1.1
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-bin-v1.1.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-v1.1.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-v1.1.zip zip]
| March 1st, 2013
|-
| 1.0.5
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.5.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.5.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.5.zip zip]
| October 23rd, 2012
|-
| 1.0.1
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.1.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.1.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.1.zip zip]
| July 6th, 2012
|-
| 1.0.0
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo-1.0.0.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_src-1.0.0.zip zip]
| [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_api-1.0.0.zip zip]
| April 26th, 2012
|-
|-
| 0.96
| 0.96
Line 56: Line 166:
<br/>
<br/>


== Manual ==
=== Requirements (for MiToBo < 1.3) ===
MiToBo requires Java 1.6 or later.
 
'''Note''': Java 1.7 is currently not fully supported!
 
The following external jars are needed to run MiToBo plugins and use the code.<br/>
<b>Note that the binary zip file already includes all jars required, there is no need for explicit download!</b>
 
MiToBo depends on the following external jars:
 
* [http://rsbweb.nih.gov/ij/ ImageJ], >= Version 1.47d
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0
* [http://xstream.codehaus.org/ XStream], Version 1.3.1
* [http://www.csie.ntu.edu.tw/~cjlin/libsvm/ LIBSVM], Version 3.1
* [http://www.loci.wisc.edu/software/bio-formats/ Loci Tools], Version 4.3.3
* [http://math.nist.gov/javanumerics/jama/ Jama], Version 1.0.2
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05
* [http://sezpoz.java.net/ SezPoz], Version 1.9
* [http://www.jgraph.com/mxdownload.html JGraph], Version 1.7.1.8


Detailed information about MiToBo, its API and usage, can be found in the user and programmer manual.  
* [https://jai-imageio.dev.java.net/ JAI ImageIO], Version 1.1 (only required for MiToBo 0.9)


* MiToBo-Manual, Version 0.9.6 [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf pdf]
=== Project internal libraries ===
<br/>


== Project internal libraries ==
MiToBo also relies on some libraries provided by the MiToBo project itself.<br>
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.


'''[[Note]]:''' <br/>
'''[[Note]]:''' <br/>
''' You do not need to download these libraries explizitly if you downloaded the zip file from above.''' <br/>
''' You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.''' <br/>
''' All project internal libraries are included there!''' <br/>


The MiToBo internal archive files included in the zip file are the following ones:


The zip files contain a selection the following jars, depending on the version of MiToBo:
* ALDGraphml, Version 1.0.0 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):
 
* ALDGraphml, Version 0.9.6 (Alida extensions for [http://graphml.graphdrawing.org/ graphML]):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/aldgraphml/aldgraphml.jar jar]
* MTBXml, Version 0.9.6 (MiToBo XML I/O for several datatypes, based on XMLBeans):
* MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar]  
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mtbxml/mtbxml.jar jar]  
* libJNI_Cgal_Polygon2D.{so|dll}:
* MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):
** native C++ library needed for snakes classes, based on CGAL classes: [http://www.informatik.uni-halle.de/mitobo/downloads/native/lib32/libJNI_Cgal_Polygon2D.so 32-bit Linux] [http://www.informatik.uni-halle.de/mitobo/downloads/native/lib64/libJNI_Cgal_Polygon2D.so 64-bit Linux] [http://www.informatik.uni-halle.de/mitobo/downloads/native/libwin32/JNI_Cgal_Polygon2D.dll 32-bit Windows]
** Binary [http://www.informatik.uni-halle.de/mitobo/downloads/mitoboHelp/MiToBo-Help.jar jar]  
 


The following library is only required for MiToBo-0.9:  
The following library is only required for MiToBo-0.9:  
Line 87: Line 212:
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
** Alternatively, the [https://imageio-ext.dev.java.net/ ImageIO-Ext] library can be used, which depends on the [https://jai-imageio.dev.java.net/ JAI ImageIO] library and the [https://jai.dev.java.net/ JAI] library.<br/>MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.
<br/>
<br/>
== Additional resources ==
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.
<br/>
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR>
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR>
* For Windows with 32-bit architecture a self extracting installer  including an executable of Chipory is available.
<br/>
Download the current release:
[http
* Chipory binary  [http://www.informatik.uni-halle.de/mitobo/downloads/Chipory.zip zip]
* self extracting installer for Windows [http://www.informatik.uni-halle.de/mitobo/downloads/chipory-setup.exe chipory-setup.exe]
Source code for Chipory is available upon request.
<br/>
'''Example images'''<br/>
* [http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]
== Logo ==
* MiToBo logo as [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.pdf PDF] or [http://www.informatik.uni-halle.de/mitobo/downloads/MiToBo_logo.png PNG]

Latest revision as of 12:02, 29 November 2023

Quick Start

The easiest and fastest way to install and run MiToBo is to activate MiToBo's update site in Fiji:

http://sites.imagej.net/MiToBo

To enable this site in your Fiji installation refer to the Fiji documentation.


For installing MiToBo this way you need to activate the following site:

  • MiToBo

For some operators additional sites are required:

  • Biomedgroup (e.g., for PaCeQuant)


More details how to install and run MiToBo can be found on our Installation page.

Downloads and Releases

The current release of the MiToBo core distribution and also of the extended MiToBo-Plugins distribution is 2.3.1.

Since release 1.3 we support Maven for managing MiToBo's resources.
You can download the MiToBo distributions as well as the Maven artifacts from our Maven server:

https://moon.informatik.uni-halle.de/#browse/de.unihalle.informatik.MiToBo

There are two MiToBo distributions available:

  • MiToBo:
    this package contains the core of MiToBo, i.e. all operators, the MiToBo runners for operator execution and also Grappa;
    not included are the plugins to run MiToBo from within ImageJ 1.x, hence, this distribution is mainly for stand-alone usage of MiToBo and development purposes
  • MiToBo-Plugins:
    this package contains the complete MiToBo distribution, some special plugins like the MTB Cell Counter, and in addition some ImageJ plugins to run MiToBo operators from within ImageJ; you should download the MiToBo-Plugins distribution if you like to use MiToBo with ImageJ

Since release 1.8 MiToBo's implementation requires at least Java 1.8.

At the bottom of this page additional files are available for download:

  • Old distributions: complete distributions including all dependencies, scripts, documentation, etc.
  • Binaries only: only the jar archives, no dependencies neither documentation
  • APIs: Javadoc APIs


Maven Project Template

Using MiToBo as a library for own developments can best be done by making use of Maven.
Particularly, Maven automatically resolves all dependencies which otherwise would have to be installed manually.

For getting started with MiToBo and Maven a project template is provided:

Maven project template [zip]

The project is readily configured and you can immediately start with own developments.
It also contains a demo operator showing the basic usage of MiToBo data types and operators on the code level.

Make sure that you have installed Maven and a Java Develpoment Kit (JDK) in version 1.8 or higher.
You can check the Java version by running 'mvn --version' from command line.
If an older Java version is used, let the 'JAVA_HOME' environment variable point to a folder containing a more recent JDK.

You can run Maven directly from within the extracted folder. Alternatively the Maven template project can easily be imported into an IDE like Eclipse.
The zip file contains a README file containing more information about installing and configuring the project template.


Manual

Detailed information about MiToBo, its API and usage, can be found in MiToBo's User and Programmer Guide.

  • MiToBo-Guide, Version 1.0 pdf


Additional resources

  • Chipory - a graph visualization tool for displaying MiToBo history graphs
    Chipory is an extended version of the Chisio software developed at the Bilkent University in Turkey.


The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.

  • To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.
  • In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.
  • For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.


Download the current release:

Source code for Chipory is available upon request.



Earlier releases of MiToBo (< 1.5)

Since release 1.3 MiToBo's resources are available from our Maven archive server: [1]
Binaries, sources and documentation for versions older than the current release, but at least of version 1.3 or newer can be found there.
All other releases can be accessed via the list below.

Version Binaries Sources API Date
1.4.3 zip jar jar March 31st, 2015 (Support for callbacks)
1.4.2 zip jar jar Jan 7th, 2015
1.4.1 zip jar jar Dec 1st, 2014
1.2 zip zip zip May 17th, 2013
1.1 zip zip zip March 1st, 2013
1.0.5 zip zip zip October 23rd, 2012
1.0.1 zip zip zip July 6th, 2012
1.0.0 zip zip zip April 26th, 2012
0.96 zip zip zip September 01, 2011
0.95 zip zip zip June 08, 2011 (updated June 22nd, 2011)
0.9 zip tar.gz zip tar.gz zip tar.gz October 26, 2010


Requirements (for MiToBo < 1.3)

MiToBo requires Java 1.6 or later.

Note: Java 1.7 is currently not fully supported!

The following external jars are needed to run MiToBo plugins and use the code.
Note that the binary zip file already includes all jars required, there is no need for explicit download!

MiToBo depends on the following external jars:

  • JAI ImageIO, Version 1.1 (only required for MiToBo 0.9)

Project internal libraries

MiToBo also relies on some libraries provided by the MiToBo project itself.
In particular XML schemes for representing the history graphs and MiToBo's online help are included in separate jar archives.

Note:
You do not need to download these libraries explicitly. If you download the binary zip file all jars and libraries are already included.

The MiToBo internal archive files included in the zip file are the following ones:

  • ALDGraphml, Version 1.0.0 (Alida extensions for graphML):
  • MTBXml, Version 1.0.0 (MiToBo XML I/O for several datatypes, based on XMLBeans):
  • MiToBo-Help, Version 1.0.0 (MiToBo JavaHelp pages):

The following library is only required for MiToBo-0.9:

  • MTBImageIO-Ext, Version 0.9 (improved image I/O based on ImageIO-Ext):
    • Binary jar
    • Source code zip
    • Alternatively, the ImageIO-Ext library can be used, which depends on the JAI ImageIO library and the JAI library.
      MTBImageIO-Ext is simply the TIFF part of ImageIO-Ext with slight adjustments to remove dependency on the JAI library.