Installation - Revision history

Moeller: /* Using MiToBo with ImageJ */

2023-11-29T10:59:17Z

Using MiToBo with ImageJ

← Older revision		Revision as of 12:59, 29 November 2023
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	== Using MiToBo with ImageJ ==		== Using MiToBo with ImageJ ==

	'''Important Note:''' These instructions refer to ImageJ 1.		'''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>		<br>

Moeller at 10:56, 29 November 2023

2023-11-29T10:56:44Z

← Older revision		Revision as of 12:56, 29 November 2023
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	Using MiToBo with a [[Installation/Windows\|Windows operating system]].		Using MiToBo with a [[Installation/Windows\|Windows operating system]].

	~~<br>~~

	~~== The MiToBo Binary Zip File ==~~

	To get the current release of MiToBo (e.g. for using it as a library for your own developments) either download and extract the MiToBo Binary zip file from [https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/] or clone our Github repository [https://github.com/mitobo-hub/mitobo https://github.com/mitobo-hub/mitobo].<br> You will find the following structure of directories and files:
	* 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
	* testimages - some sample images
	* ''MiToBo-Guide-1.0.pdf'' - the user and programmer guide for MiToBo
	* ''oprunner.sh'' - shell script to run MiToBo operators from commandline (Linux only)
	* ''run.sh'' - shell script to run ImageJ with MiToBo (Linux only)
	* ''README'' - with basic information

	~~== Using MiToBo's APIs ==~~
	To use the API of MiToBo and benefit from MiToBo's functionality in your own code you just need to make the jar archive to be found in the zip file available on your classpath. In addition, make sure that all jar archives MiToBo depends on and which are listed on the [[downloads\|Download page]] are also in your classpath.<br> Note that the jars are also included in the MiToBo's binary zip file, thus, you don't need to download them manually.

Moeller: /* The MiToBo Binary Zip File */

2023-11-29T10:56:20Z

The MiToBo Binary Zip File

← Older revision		Revision as of 12:56, 29 November 2023
Line 67:		Line 67:
	== The MiToBo Binary Zip File ==		== The MiToBo Binary Zip File ==

	To get the current release of MiToBo download and extract the MiToBo Binary zip file from [https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/].<br> You will find the following structure of directories and files:		To get the current release of MiToBo (e.g. for using it as a library for your own developments) either download and extract the MiToBo Binary zip file from [https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/] or clone our Github repository [https://github.com/mitobo-hub/mitobo https://github.com/mitobo-hub/mitobo].<br> You will find the following structure of directories and files:
	* lib - includes nesessary libaries for Linux and Windows		* lib - includes nesessary libaries for Linux and Windows
	* licences - includes MiToBo license and licences for other software used by MiToBo		* licences - includes MiToBo license and licences for other software used by MiToBo

Moeller at 10:54, 29 November 2023

2023-11-29T10:54:25Z

← Older revision		Revision as of 12:54, 29 November 2023
Line 67:		Line 67:
	== The MiToBo Binary Zip File ==		== The MiToBo Binary Zip File ==

	To get the current release of MiToBo download and extract the MiToBo Binary zip file from .<br> You will find the following structure of directories and files:		To get the current release of MiToBo download and extract the MiToBo Binary zip file from [https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/ https://moon.informatik.uni-halle.de/repository/releases/de/unihalle/informatik/MiToBo/mitobo/].<br> You will find the following structure of directories and files:
	* lib - includes nesessary libaries for Linux and Windows		* lib - includes nesessary libaries for Linux and Windows
	* licences - includes MiToBo license and licences for other software used by MiToBo		* licences - includes MiToBo license and licences for other software used by MiToBo

Moeller: /* The MiToBo Binary Zip File */

2023-11-29T10:53:20Z

The MiToBo Binary Zip File

← Older revision		Revision as of 12:53, 29 November 2023
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	<br>		<br>

	== The ~~[[downloads\|~~MiToBo Binary]] Zip File ==		== The MiToBo Binary Zip File ==

	To get the current release of MiToBo download and extract the ~~[[downloads\|~~MiToBo Binary zip file]].<br> You will find the following structure of directories and files:		To get the current release of MiToBo download and extract the MiToBo Binary zip file from .<br> You will find the following structure of directories and files:
	* lib - includes nesessary libaries for Linux and Windows		* lib - includes nesessary libaries for Linux and Windows
	* licences - includes MiToBo license and licences for other software used by MiToBo		* licences - includes MiToBo license and licences for other software used by MiToBo

Moeller: /* Using MiToBo with ImageJ */

2023-11-29T10:51:55Z

Using MiToBo with ImageJ

← Older revision		Revision as of 12:51, 29 November 2023
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	== Using MiToBo with ImageJ ==		== Using MiToBo with ImageJ ==

	'''Important Note:''' These instructions refer to ImageJ 1 ~~only, instructions for ImageJ 2.0 will follow soon~~.		'''Important Note:''' These instructions refer to ImageJ 1.

	<br>		<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 ===		=== Linux ===

Moeller: /* General remarks */

2023-11-29T10:48:24Z

General remarks

← Older revision		Revision as of 12:48, 29 November 2023
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	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.		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.

	<br>		<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".

			[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].

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

	== Using MiToBo with Fiji ==		== Using MiToBo with Fiji ==

Moeller: /* General remarks */

2023-11-29T10:44:18Z

General remarks

← Older revision		Revision as of 12:44, 29 November 2023
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	<br>		<br>

	== Using MiToBo with Fiji ==		== 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>		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>

Moeller: /* Using MiToBo with Fiji */

2019-01-22T11:35:42Z

Using MiToBo with Fiji

← Older revision		Revision as of 13:35, 22 January 2019
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	<li> For some of our operators special issues exist and require special treatment:		<li> For some of our operators special issues exist and require special treatment:
	<ul>		<ul>
	<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		<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
	</ul>		</ul>
	</ul>		</ul>

	<br>		<br>

	== Using MiToBo with ImageJ ==		== Using MiToBo with ImageJ ==

Moeller at 11:34, 22 January 2019

2019-01-22T11:34:33Z

← Older revision		Revision as of 13:34, 22 January 2019
Line 8:		Line 8:
	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.		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.

			<br>
	== Using MiToBo with Fiji ==		== 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>		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>
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	</ul>		</ul>

			<br>
	== Using MiToBo with ImageJ ==		== Using MiToBo with ImageJ ==