Installation: Difference between revisions

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== Linux ==
== General remarks ==


... comming soon!
There are two common ways to work with MiToBo:
<ul>
<li> just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji
<li> using the MiToBo API to write operators, plugins and other image analysis applications on your own
</ul>
The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.<br> Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.


== Windows ==
<blockquote style="background-color: lightgrey; border: solid thin grey;">
'''[[The recommended way to install and run MiToBo and its operators/plugins is via Fiji!]]'''<br>
MiToBo has its own Fiji update site named "MiToBo".


After downloading and extracting the [[downloads|MiToBo Binaries zip]] you will find the following structure in the ''MiToBo-bin'' directory
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]<br>


* docs - includes the MiToBo manual
To enable this site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].
* lib - includes nesessary libaries for Linux and Windows
* licences - includes MiToBo license and licences for other software used by MiToBo
* macros - includes the MiToBo macro toolset
* plugins - includes MiToBo jar and other jars used by MiToBo
* oprunner.sh and run.sh - scripts for Linux OS


Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.
</blockquote>


For installing MiToBo into an existing ImageJ installation perform the following steps:
== Using MiToBo with Fiji ==
Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation. <br> The MiToBo update site is<br>


# go to the '''MiToBo-bin/plugins/''' directory
[http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo]
#* copy the ''Mi_To_Bo.jar'' to your ''../ImageJ/plugins/'' directory (''C:\Program Files\ImageJ\plugins'' by default)
 
#* copy all jars to your ''../ImageJ/plugins/jars/'' directory <span style="text-decoration: underline;">except</span> the ij.jar and jars already existing<br/>('''Notice:''' MiToBo [[downloads|requires]] explicite versions of some jars, other versions may not work probably!)<br/><br/>
To enable the site in your Fiji installation refer to the [http://fiji.sc/How_to_follow_a_3rd_party_update_site Fiji documentation].
# go to the '''MiToBo-bin/lib/''' directory
 
#* copy the ''libwin32'' directory to your ''../ImageJ/'' directory<br/><br/>
'''Important notices:'''<br>
# go to the '''MiToBo-bin/macros/toolsets/''' directory
<ul>
#* copy the ''MiToBo_Runner.txt'' to your ''../ImageJ/macros/toolsets/'' directory<br/><br/>
<li> Occasionally MiToBo '''operators crash when run from within Fiji'''. The reason for this behaviour are most of the time '''conflicting jar archives''' delivered with the Fiji distribution.<br> We figured out that particularly the jar file
# configurate your ImageJ startup<br/><br/>
 
:* update ImageJ configuration file ''../ImageJ/ImageJ.cfg'' an add the following line<br/><br/>'''-Djava.library.path="C:\Programme\ImageJ\libwin32" -cp "C:\Programme\ImageJ\ij.jar" ij.ImageJ'''<br\><br/>('''Notice:''' The ImageJ directory path depends on your ImageJ installation)<br/><br/>Example of an ImageJ.cfg file:
* jars/bio-formats/formats-common-5.1.x.jar
    C:\Program Files\ImageJ\
 
    C:\Program Files\Java\jre6\bin\javaw.exe
often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.
    -Djava.library.path="C:\Program Files\ImageJ\libwin32" -cp "C:\Program Files\ImageJ\ij.jar" ij.ImageJ
<li> For some of our operators special issues exist and require special treatment:
<br/>
<ul>
:* as an alternative you can start ImageJ from command line
<li> [[Applications/CellBoundaryExtractor2D| CellBoundaryExtractor2D]]: there are version conflicts with regard to the '''JGraphT library''' used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the [[Applications/CellBoundaryExtractor2D|webpage of the operator]] for a workaround
::* open your Windows command line
</ul>
::* move to the ''../ImageJ/'' directoy
</ul>
::* type the following command:
 
  java -Djava.library.path="C:\Program Files\ImageJ\libwin32" -cp "C:\Program Files\ImageJ\ij.jar" ij.ImageJ
<br>
 
== Using MiToBo with ImageJ ==
 
'''Important Note 1:''' Before you consider installing MiToBo manually within ImageJ, check if it could not be an option to use Fiji and activate MiToBo's update site - in most cases this will be significantly less painful...
 
'''Important Note 2:''' These instructions refer to ImageJ 1.
 
<br>
General remarks:<br>
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from<br>
 
[https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/]<br>
 
which already includes '''''all''''' dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.
 
=== Linux ===
 
Using MiToBo with a [[Installation/Linux|Linux operating system]].
 
<br>
 
=== Windows ===
 
Using MiToBo with a [[Installation/Windows|Windows operating system]].

Latest revision as of 11:59, 29 November 2023

General remarks

There are two common ways to work with MiToBo:

  • just using the operators included in MiToBo for improving your work and easing image processing tasks, e.g., via ImageJ or Fiji
  • using the MiToBo API to write operators, plugins and other image analysis applications on your own

The functionality of MiToBo is best used from within ImageJ or Fiji. In case that you aim to use MiToBo for your own development, you need to download the binaries explicitly. The actual installation instructions differ in some parts depending on which way of using MiToBo you have in mind.
Below we will first outline more details about the installation steps required for simply using MiToBo's operators in ImageJ and Fiji, and then provide some notes regarding the binary zip file. Finally we will present some details for using MiToBo's API with your own code.

The recommended way to install and run MiToBo and its operators/plugins is via Fiji!
MiToBo has its own Fiji update site named "MiToBo".

http://sites.imagej.net/MiToBo

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

Note that for some plugins (e.g., PaCeQuant) also the "Biomedgroup" update site needs to be activated.

Using MiToBo with Fiji

Since release 1.5 MiToBo features a Fiji update site and the easiest way to use MiToBo's operators and plugins is to enable the update site in your Fiji installation.
The MiToBo update site is

http://sites.imagej.net/MiToBo

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

Important notices:

  • Occasionally MiToBo operators crash when run from within Fiji. The reason for this behaviour are most of the time conflicting jar archives delivered with the Fiji distribution.
    We figured out that particularly the jar file
    • jars/bio-formats/formats-common-5.1.x.jar
    often causes such trouble. Thus, if you encounter problems running MiToBo operators, please try to locally delete or uninstall the abovementioned jar archive from your local Fiji installation and then re-run the MiToBo operator.
  • For some of our operators special issues exist and require special treatment:
    • CellBoundaryExtractor2D: there are version conflicts with regard to the JGraphT library used by this operator and also by default included in every Fiji distribution; please refer to installation instructions on the webpage of the operator for a workaround


Using MiToBo with ImageJ

Important Note 1: Before you consider installing MiToBo manually within ImageJ, check if it could not be an option to use Fiji and activate MiToBo's update site - in most cases this will be significantly less painful...

Important Note 2: These instructions refer to ImageJ 1.


General remarks:
For using MiToBo with ImageJ it is the easiest to download the latest distribution zipfile (*-bin.zip) from

https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/

which already includes all dependencies and ships with some scripts to run MiToBo's operators and plugins out of the box.

Linux

Using MiToBo with a Linux operating system.


Windows

Using MiToBo with a Windows operating system.

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