Moeller: Created page with "== MTBCellCounter 1.0 (part of MiToBo 1.8.8 and earlier) == link= This page provides the documentation for the old version (availa..."

2018-04-25T12:00:13Z

Created page with "== MTBCellCounter 1.0 (part of MiToBo 1.8.8 and earlier) == 350px|right|link= This page provides the documentation for the old version (availa..."

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== MTBCellCounter 1.0 (part of MiToBo 1.8.8 and earlier) ==
[[File:ScreenshotCellCounter.png|350px|right|link=]]

This page provides the documentation for the old version (available in MiToBo 1.8.8 and earlier) of the MTBCellCounter plugin.

The plugin got an update in MiToBo 1.8.9. The documentation for the new version can be found [[Applications/MTBCellCounter|here]].

===== Related Publications=====
* ''L. Franke, B. Storbeck, J. L. Erickson, D. Rödel, D. Schröter, B. Möller, and M. H. Schattat''. ''' ''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.'' ''' Journal of Endocytobiosis and Cell Research, 26:31-42, 2015, [http://zs.thulb.uni-jena.de/receive/jportal_jparticle_00342296 Online version].

===== Name of Plugin/Operator =====
<code>
mtb_cellcounter.MTB_CellCounter
</code>
 
(available in MiToBo-Plugins since version 1.5)
 

===== Download and Installation =====
For a quick start you best download the MiToBo-Plugins zip file from [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/MiToBo/mitobo-plugins/1.5/mitobo-plugins-1.5-bin.zip here]. On Linux and Mac OS systems just unzip the file in an empty directory of your choice and start ImageJ by running the "run.sh" script included in the zip file.
On Windows machines it is easiest to first install ImageJ or Fiji and then follow the instructions given [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Installation#Windows here].

Note that the native libraries are not required for running the MTB_CellCounter plugin.

Further information on how to install MiToBo in general can be found on the [http://www2.informatik.uni-halle.de/agprbio/mitobo/index.php/Installation Installation page].

Once MiToBo is installed, you can start the MTB_CellCounter from the "Plugins" menu, item MiToBo, then "MTB CellCounter".

===== Usage =====
For using the plugin you need to install MiToBo by following the instructions on the [[Installation]] page. Running ImageJ you will then find a new entry ''MiToBo'' in the plugins menu from where you can select the ''MTB CellCounter'' plugin.

The usage of the plugin is leaned on the usage of the original plugin (see also [http://rsb.info.nih.gov/ij/plugins/cell-counter.html Cell Counter webpage]).

The basic workflow is as follows:
* open the image you would like to process and press the '' 'Initialize' '' button
* optionally configure the particle detector via the '' 'Configure operator...' '' button and then press '' 'Detect' ''
* once the detection is finished you can filter detected particles via the '' 'Filter Particles...' '' button by size and average intensity; if you are done, press '' 'Select Markers' ''
* now markers can manually be edited, i.e. markers can be added or removed, or their type can be changed
* at the end you can view marker statistics (button '' 'Results' ''), save the markers to a file (button '' 'Save Markers' '') or do some measurements (button '' 'Measurements...' '')

===== Functions and Options =====
Below we outline the functions of the various elements of the graphical user interface.

* '''Initialization:'''
** '' 'Initialize' '': initializes the plugin with the active image, if the image has more than one channel only the first channel is considered
** '' 'Keep original' '': if checked the source image remains open, otherwise it is closed

[[File:ScreenshotParticleFilter.png|250px|right|link=]]
* '''Pre-segmentation:'''
** '' 'Detect' '': runs the particle detector
** '' 'Configure Operator...' '': allows to change the parameters of the particle detector (see below)
** '' 'Filter Particles...' '': allows to filter detection results
** '' 'Show contours' '': enables/disables display of the contours of detected particle regions
** '' 'Select markers' '': selects the final set of markers and terminates detection stage

Detected particles are labeled with marker type 1 and the counter of that type refers to their number.

* '''Marker management and editing:'''
** '' 'Add' '': add a new marker type at the end of the list, the type gets a random color
** '' 'Remove' '': delete the last type from the end of the list
** '' 'Delete' '': delete the last placed marker
** '' 'Reset' '': deletes all markers
** '' 'Show Markers' '': enables/disables display of markers
** '' 'Show Numbers' '': enables/disables display of marker numbers
** '' 'Show All' '': enables/disables display of both markers and numbers

Note that the currently selected marker type and the settings for showing markers and numbers are also displayed in the status bar of the image window. 
Some additional actions for editing markers are available via keyboard shortcuts and mouse actions only, see below.

* '''Results:'''
** '' 'Results' '': shows table with marker statistics
** '' 'Save Markers' '': saves the markers to an XML file
** '' 'Load Markers' '': loads markers from an XML file
** '' 'Export Image' '': save a copy of the image including all markers

 
[[File:ScreenshotConfigurationDetector.png|350px|right|link=]]
For the pre-segmentation of spot-like structures a particle detector operator of MiToBo is used. It has been published in 
''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'', ''' ''Scale-adaptive Wavelet-based Particle Detection in Microscopy Images,'' ''' 
Proc. of Workshop Bildverarbeitung für die Medizin (BVM '10), Hans-Peter Meinzer, Thomas Martin Deserno, Heinz Handels, and Thomas Tolxdorff, editors, 
Springer, Informatik Aktuell, pp. 266-270, Aachen, Germany, March 2010.

The operator offers the following parameters:
{|class="wikitable"
|Name
|Description
|-
|''Minimal Scale (JMin)''
|scale of smallest particles, set to an integer value >= 1
|-
|''Maximal Scale (JMax)''
|scale of largest particles, set to an integer value > JMin
|-
|''Scale Interval Size''
|several adjacent scales are correlated, the interval size determines how many scales are considered for each correlation
|-
|''Correlation Threshold''
|threshold for detecting particles, the smaller the threshold is chosen the more particles will be detected
|-
|''Minimum Region Size''
|minimal size of valid particles (in pixels), smaller particles are discarded
|}

===== Keyboard Shortcuts and Mouse Actions =====
{|class="wikitable"
|Key
|Description
|-
|''1-9''
|select the corresponding marker type
|-
|''a'' or ''left arrow''
|scroll image to the left
|-
|''d'' or ''right arrow''
|scroll image to the right
|-
|''e''
|zoom out
|-
|''q''
|zoom in
|-
|''s'' or ''arrow down''
|scroll downwards
|-
|''w'' or ''arrow up''
|scroll upwards
|-
|''v''
|enable/disable display of contours (only after detected markers are selected)
|-
|''x''
|enable/disable display of numbers
|-
|''y''
|enable/disable display of markers
|}

In edit mode the following mouse actions are available:
* ''left mouse button'': place a new marker of currently selected type
* ''right mouse button'': delete nearest marker of currently selected type
* ''Strg'' + ''left mouse button'': change type of nearest marker (with a different type) to currently selected type
* ''Shift'' + ''left mouse button'': draw a closed region of interest, all markers inside the region are removed

===== Sample data =====
For testing you can use the following set of sample images:

* [http://www2.informatik.uni-halle.de/mitobo/downloads/CellCounter-SampleImages.zip Cell counter sample images]

Applications/MTBCellCounter 1.0 - Revision history

Moeller: Created page with "== MTBCellCounter 1.0 (part of MiToBo 1.8.8 and earlier) == link= This page provides the documentation for the old version (availa..."