Main Page: Difference between revisions

From MiToBo
Jump to navigationJump to search
No edit summary
(44 intermediate revisions by the same user not shown)
Line 1: Line 1:
= MiToBo - A <span style="color:#CC0000">m</span>icroscope <span style="color:#CC0000">i</span>mage analysis <span style="color:#CC0000">to</span>ol<span style="color:#CC0000">bo</span>x =
= MiToBo - A <span style="color:#CC0000">m</span>icroscope <span style="color:#CC0000">i</span>mage analysis <span style="color:#CC0000">to</span>ol<span style="color:#CC0000">bo</span>x =
{| width="100%"
 
|-
{|width="100%"
|style="vertical-align:top" |
|-
|style="vertical-align:top" |
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''What is MiToBo?'''<br>
The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ] and its new release [http://developer.imagej.net/ ImageJ 2.0].<br />  
The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application [http://rsbweb.nih.gov/ij/ ImageJ] and its new release [http://developer.imagej.net/ ImageJ 2.0].<br />  
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various  
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various  
Line 18: Line 20:
Furthermore, MiToBo offers a user- and programmer friendly framework for developing algorithms that have properties not available in ImageJ, <br />
Furthermore, MiToBo offers a user- and programmer friendly framework for developing algorithms that have properties not available in ImageJ, <br />
however, still provides full compatibility to all ImageJ features. <br />
however, still provides full compatibility to all ImageJ features. <br />
<p>
<p>
MiToBo completely separates the implementation of image processing algorithms from potential user interfaces.<br />  
MiToBo completely separates the implementation of image processing algorithms from potential user interfaces.<br />  
Line 30: Line 31:
</ul>
</ul>
</p>
</p>
<p>
<p>
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.
</p>
</div>
</div>
<br>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''Visit MiToBo also at...'''<br>
{|
|style="text-align:center;width:10%"|[[file:Imagej-128.png|90px|link=http://imagej.net/MiToBo]]
|style="text-align:center;width:10%"|[[file:logo.png|90px|link=http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start]]
|style="text-align:center;width:10%"|[[file:logo-blue.png|90px|link=https://omictools.com/microscope-image-analysis-toolbox-tool]]
|style="text-align:center;width:10%"|[[file:Git.png|90px|link=https://github.com/mitobo-hub]]
|-
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]
|style="text-align:center;width:10%"|[http://imagejdocu.tudor.lu/doku.php?id=plugin:collections:mitobo_-_a_microscope_image_analysis_toolbox:start ImageJ Docu Wiki]
|style="text-align:center;width:10%"|[https://omictools.com/microscope-image-analysis-toolbox-tool OMIC Tools]
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]
|}
</div>
</div>
|
|
|style="vertical-align:top" |
|style="vertical-align:top" |
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''Download'''<br>
'''How to get MiToBo?'''<br>
You can download MiToBo version 1.5 [[Downloads | here]]. <br />
* ImageJ-Users:<br> download the [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.8.7.1/mitobo-plugins-1.8.7.1-bin.zip MiToBo-Plugins package] and follow the installation instructions to be found [[Installation | here]].
You can find the API documentation for this release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/>
* Fiji-Users:<br> simply add MiToBo's update site [http://sites.imagej.net/MiToBo http://sites.imagej.net/MiToBo] to your Fiji installation
* use in general:<br> you can download MiToBo and the MiToBo plugins package [[Downloads | here]]. <br/>  
 
You can find the API documentation for this release [http://www.informatik.uni-halle.de/mitobo/api/index.html here].<br/>  
Furthermore MiToBo offers you a user and programmer guide<br> which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].
Furthermore MiToBo offers you a user and programmer guide<br> which you can download [http://www.informatik.uni-halle.de/mitobo/downloads/manual/MiToBoManual.pdf here].
</div>
</div>
Line 47: Line 70:
<div style="padding: 0.3em 1em 0.7em 1em;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''Latest News'''<br>
'''Latest News'''<br>
* June 2015: Version 1.5 of MiToBo has been released. <br/>
* 05/2018: MiToBo 1.8.9 and MiToBo-Plugins 1.8.9 have been released mainly featuring an update of our MTBCellCounter tool.
This release ships with the new [[Applications/MTBCellCounter | MTB Cell Counter]] plugin for semi-automatic segmentation and annotation of cell images. Details about the plugin
* 01/2018: MiToBo 1.8.7 and MiToBo-Plugins 1.8.7.1 have been released mainly featuring improved support for commandline data I/O of operators.<br>Note that from now on MiToBo releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.
(derived from the [http://fiji.sc/Cell_Counter CellCounter plugin] written by Kurt de Vos) can be found on the [[Applications/MTBCellCounter | MTB Cell Counter wikipage]] and in the corresponding paper of Franke et al., "''The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes''.", which just appeared in the Journal of Endocytobiosis and Cell Research, (26) 31-42, 2015, to be found [http://zs.thulb.uni-jena.de/receive/jportal_jparticle_00342296 here].
* 09/2017: MiToBo and MiToBo-Plugins 1.8.6 have been released! The new release includes [[Applications/PaCeQuant | PaCeQuant ]], our new tool for high-throughput quantification of pavement cell shape.


* March 2015: Version 1.4.3 of MiToBo has been released. <br/>
The news archive can be found [[News Archive | here]].
The most important new feature is support for parameter callbacks. Based upon Alida in version 2.5 and its support for callbacks it is now possible to update the values of operator parameters depending on changes of other parameters. In addition, callbacks enable dynamic changes of the set of parameters an operator owns and dynamic re-configuration of the graphical interfaces, respectively.
</div>
 
</div>
* January 2015: Version 1.4.2 of MiToBo has been released. <br/>
<br>
 
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
* December 2014: Version 1.4.1 of MiToBo has been released. <br/>
<div style="padding: 0.3em 1em 0.7em 1em;">
MiToBo and its base Alida will be presented at the OGRW 2014, which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding. The workshop is taking place from 1st to 5th December in Koblenz/Germany.  
'''Licensing information'''<br>
The title of our contribution is '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms.'''''
MiToBo is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].
 
</div>
* July 2014: Version 1.4 of MiToBo has been released. <br/>
</div>
The new version ships with new tools for the quantification of actin structures in microscopy images of cells, the ''[[Applications/ActinAnalyzer2D | ActinAnalyzer2D]]'', and a new operator for detecting Xylems in images of cross sections of wood.
<br>
 
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
* January 2014: Version 1.3 of MiToBo has been released. <br/>
<div style="padding: 0.3em 1em 0.7em 1em;">
The project management of MiToBo switched to Maven, from now on you can download MiToBo releases from our [https://moon.informatik.uni-halle.de/archiva/browse/de.unihalle.informatik.MiToBo Maven server].<br> The new release ships with a new version of the ''[[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]'' and includes the first release of the ''CellMigrationAnalyzer'',<br> a tool for cell tracking and migration analysis. In addition, in the MiToBo core several bugs were fixed, an illumination correction and a<br> top-hat based contrast enhancement were added.
'''Gnu PGP Public Key'''<br>
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's [https://pgp.mit.edu/pks/lookup?op=get&search=0x259F7DD171EFF7A9 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.
</div>
</div>
<br>
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;">
<div style="padding: 0.3em 1em 0.7em 1em;">
'''Bug reports & Feature requests'''<br>
Bug reports and feature requests can be submitted as issues on [https://github.com/mitobo-hub/mitobo/issues Github] or by mail to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de]. Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted.
</div>
</div>
</div>
</div>
|}
|}
== News Archive ==
The news archive can be found [[News Archive | here]].
== Licensing information ==
MiToBo is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].
== Bug reports & Feature requests ==
Bug reports and feature requests can be submitted via the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/bug_report_page.php MiToBo bugtracking system] or by mail to [mailto:mitobo@informatik.uni-halle.de mitobo@informatik.uni-halle.de].<br />
Before reporting a new bug, please check if that bug has already been submitted in the [http://www2.informatik.uni-halle.de/agprbio/mitobo-bts/view_all_bug_page.php report list].<br />

Revision as of 13:41, 4 May 2018

MiToBo - A microscope image analysis toolbox

What is MiToBo?
The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0.
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes.
Some of MiToBo's operators are for example these ones:

  • ActinAnalyzer for the quantification of actin filament structures in microscopy images
  • Cell Migration Analyzer for analyzing single cell migration from time lapse image sequences
  • Neuron Analyzer for the segmentation of neurons in microscope images
  • Scratch Assay Analyzer for analyzing microscope images from collective cell migration experiments
  • Snake Optimizer for performing image segmentation based on explicit active contours

Furthermore, MiToBo offers a user- and programmer friendly framework for developing algorithms that have properties not available in ImageJ,
however, still provides full compatibility to all ImageJ features.

MiToBo completely separates the implementation of image processing algorithms from potential user interfaces.
Moreover, MiToBo builds on top of Alida which is a library for easing the development of data analysis algorithms and tools.
The main concept of Alida are operators as the core units for implementing data analysis algorithms.
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like

  • automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs
  • automatic generation of commandline and graphical user interfaces
  • a graphical programming editor named Grappa automatically considering all implemented operators as potential processing nodes

MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.


Visit MiToBo also at...

Imagej-128.png Logo.png Logo-blue.png Git.png
ImageJ.net ImageJ Docu Wiki OMIC Tools GitHub

How to get MiToBo?

You can find the API documentation for this release here.
Furthermore MiToBo offers you a user and programmer guide
which you can download here.


Latest News

  • 05/2018: MiToBo 1.8.9 and MiToBo-Plugins 1.8.9 have been released mainly featuring an update of our MTBCellCounter tool.
  • 01/2018: MiToBo 1.8.7 and MiToBo-Plugins 1.8.7.1 have been released mainly featuring improved support for commandline data I/O of operators.
    Note that from now on MiToBo releases are PGP signed. MiToBo's public key for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.
  • 09/2017: MiToBo and MiToBo-Plugins 1.8.6 have been released! The new release includes PaCeQuant , our new tool for high-throughput quantification of pavement cell shape.

The news archive can be found here.


Licensing information
MiToBo is free software: you can redistribute it and/or modify under the terms of the GNU General Public License version 3 or (at your option) any later version as published by the Free Software Foundation.


Gnu PGP Public Key
Since version 1.8.7 MiToBo and MiToBo-Plugins releases are PGP signed. MiToBo's public key for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.


Bug reports & Feature requests
Bug reports and feature requests can be submitted as issues on Github or by mail to mitobo@informatik.uni-halle.de. Before reporting a new bug or requesting a new feature, please check if that bug has already been submitted.