Applications/MTBCellCounter - Revision history

Moeller: /* Particles with UWT */

2018-04-25T13:13:53Z

Particles with UWT

← Older revision		Revision as of 15:13, 25 April 2018
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	<br>		<br>

	The operator targets at spot-like structures over multiple scales. It basically relies on an undecimated wavelet transformation combined with a probabilistic framework to determine for each detection event the optimal scale.		The operator targets at spot-like structures over multiple scales. It basically relies on an undecimated wavelet transformation (UWT) combined with a probabilistic framework to determine for each detection event the optimal scale.
	The operator offers the following parameters:		The operator offers the following parameters:
	{\|class="wikitable"		{\|class="wikitable"

Moeller: /* Particles with UWT */

2018-04-25T13:13:29Z

Particles with UWT

← Older revision		Revision as of 15:13, 25 April 2018
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	==== Particles with UWT ====		==== Particles with UWT ====
	[[File:MiToBoCellCounter-UWTDetector.png\|350px\|right\|link=]]		[[File:MiToBoCellCounter-UWTDetector.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<br>		For the pre-segmentation of spot-like structures a particle detector operator available in the core of MiToBo is used. It has been published in<br>

	''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'',<br>		''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'',<br>

Moeller: /* Particles with UWT */

2018-04-25T13:12:32Z

Particles with UWT

← Older revision		Revision as of 15:12, 25 April 2018
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	[[File:MiToBoCellCounter-UWTDetector.png\|350px\|right\|link=]]		[[File:MiToBoCellCounter-UWTDetector.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<br>		For the pre-segmentation of spot-like structures a particle detector operator of MiToBo is used. It has been published in<br>
	''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'', ''' ''Scale-adaptive Wavelet-based Particle Detection in Microscopy Images,'' '''<br>
			''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'',<br>
			''' ''Scale-adaptive Wavelet-based Particle Detection in Microscopy Images,'' '''<br>
	Proc. of Workshop Bildverarbeitung für die Medizin (BVM '10), Hans-Peter Meinzer, Thomas Martin Deserno, Heinz Handels, and Thomas Tolxdorff, editors,<br>		Proc. of Workshop Bildverarbeitung für die Medizin (BVM '10), Hans-Peter Meinzer, Thomas Martin Deserno, Heinz Handels, and Thomas Tolxdorff, editors,<br>
	Springer, Informatik Aktuell, pp. 266-270, Aachen, Germany, March 2010.		Springer, Informatik Aktuell, pp. 266-270, Aachen, Germany, March 2010.
			<br>

			The operator targets at spot-like structures over multiple scales. It basically relies on an undecimated wavelet transformation combined with a probabilistic framework to determine for each detection event the optimal scale.
	The operator offers the following parameters:		The operator offers the following parameters:
	{\|class="wikitable"		{\|class="wikitable"
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	\|-		\|-
	\|''Minimal Scale (JMin)''		\|''Minimal Scale (JMin)''
	\|scale of smallest ~~particles~~, set to an integer value >= 1		\|scale of smallest objects, set to an integer value >= 1
	\|-		\|-
	\|''Maximal Scale (JMax)''		\|''Maximal Scale (JMax)''
	\|scale of largest ~~particles~~, set to an integer value > JMin		\|scale of largest objects, set to an integer value > JMin
	\|-		\|-
	\|''Scale Interval Size''		\|''Scale Interval Size''
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	\|-		\|-
	\|''Correlation Threshold''		\|''Correlation Threshold''
	\|threshold for detecting ~~particles~~, the smaller the threshold is chosen the more ~~particles~~ will be detected		\|threshold for detecting objects, the smaller the threshold is chosen the more objects will be detected
	\|-		\|-
	\|''Minimum Region Size''		\|''Minimum Region Size''
	\|minimal size of valid ~~particles~~ (in pixels), smaller ~~particles~~ are discarded		\|minimal size of valid objects (in pixels), smaller objects are discarded
	\|}		\|}
	<br>		<br>

Moeller: /* Particles with UWT */

2018-04-25T13:08:42Z

Particles with UWT

← Older revision		Revision as of 15:08, 25 April 2018
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	For detecting structures in the image the plugin provides a set of detectors which are described in more detail below.		For detecting structures in the image the plugin provides a set of detectors which are described in more detail below.
	==== Particles with UWT ====		==== Particles with UWT ====
	[[File:~~ScreenshotConfigurationDetector~~.png\|350px\|right\|link=]]		[[File:MiToBoCellCounter-UWTDetector.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<br>		For the pre-segmentation of spot-like structures a particle detector operator of MiToBo is used. It has been published in<br>
	''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'', ''' ''Scale-adaptive Wavelet-based Particle Detection in Microscopy Images,'' '''<br>		''O. Greß, B. Möller, N. Stöhr, S. Hüttelmaier and S. Posch'', ''' ''Scale-adaptive Wavelet-based Particle Detection in Microscopy Images,'' '''<br>

Moeller: /* MTB Cell Counter */

2018-04-25T13:06:43Z

MTB Cell Counter

← Older revision		Revision as of 15:06, 25 April 2018
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	* advanced editing of markers		* advanced editing of markers
	* status bar, tooltips and keyboard shortcuts		* status bar, tooltips and keyboard shortcuts
			<br>

	=== News ===		=== News ===
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	Documentation for the old version (available in MiToBo 1.8.8 and earlier) is still available [[Applications/MTBCellCounter_1.0\|here]].		Documentation for the old version (available in MiToBo 1.8.8 and earlier) is still available [[Applications/MTBCellCounter_1.0\|here]].
			<br>

	=== Related Publications ===		=== 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].		* ''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].
			<br>

	=== Name of MiToBo Plugin/Operator ===		=== Name of MiToBo Plugin/Operator ===
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	<br>		<br>
	(version 1.0 is available in MiToBo-Plugins since version 1.5, an updated version was released in MiToBo/MiToBo-Plugins 1.8.9)		(version 1.0 is available in MiToBo-Plugins since version 1.5, an updated version was released in MiToBo/MiToBo-Plugins 1.8.9)
			<br>
	<br>		<br>

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	* ''Shift'' + ''left mouse button'': draw a closed region of interest, all markers inside the region are removed		* ''Shift'' + ''left mouse button'': draw a closed region of interest, all markers inside the region are removed
	* '''''Shift'' + ''Ctrl'' + ''left mouse button'': add a new marker (for a region) by drawing its contour'''		* '''''Shift'' + ''Ctrl'' + ''left mouse button'': add a new marker (for a region) by drawing its contour'''
			<br>

	=== Available Detectors ===		=== Available Detectors ===
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	\|minimal size of valid particles (in pixels), smaller particles are discarded		\|minimal size of valid particles (in pixels), smaller particles are discarded
	\|}		\|}
			<br>

	=== Sample data ===		=== Sample data ===

Moeller: /* Functions and Options */

2018-04-25T13:03:44Z

Functions and Options

← Older revision		Revision as of 15:03, 25 April 2018
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	* '''Configuration of input image:'''		* '''Configuration of input image:'''
	** ''"Channel to process"'': here you can select on which channel your are going to work if your image has more than one channel; note that you can freely switch between the channels while labeling your objects		** '''''"Channel to process"''''': here you can select on which channel your are going to work if your image has more than one channel; note that you can freely switch between the channels while labeling your objects
	** ''"Boundary Channel (opt)"'': for labeling sub-cellular objects it is possible to overlay the image with cell contours for easier orientation;<br>the contours have to be provided in binary format in one of the channels of the input image where the background should have zero intensity and the boundaries be labeled with a unique intensity or color value greater than zero		** '''''"Boundary Channel (opt)"''''': for labeling sub-cellular objects it is possible to overlay the image with cell contours for easier orientation;<br>the contours have to be provided in binary format in one of the channels of the input image where the background should have zero intensity and the boundaries be labeled with a unique intensity or color value greater than zero

	[[File:ScreenshotParticleFilter.png\|250px\|right\|link=]]		[[File:ScreenshotParticleFilter.png\|250px\|right\|link=]]

Moeller: /* Keyboard Shortcuts and Mouse Actions */

2018-04-25T13:02:17Z

Keyboard Shortcuts and Mouse Actions

← Older revision		Revision as of 15:02, 25 April 2018
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	* ''Strg'' + ''left mouse button'': change type of nearest marker (with a different type) to 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		* ''Shift'' + ''left mouse button'': draw a closed region of interest, all markers inside the region are removed
	* ''Shift'' + ''Ctrl'' + ''left mouse button'': add a new marker (for a region) by drawing its contour		* '''''Shift'' + ''Ctrl'' + ''left mouse button'': add a new marker (for a region) by drawing its contour'''

	=== Available Detectors ===		=== Available Detectors ===

Moeller: /* Keyboard Shortcuts and Mouse Actions */

2018-04-25T13:02:01Z

Keyboard Shortcuts and Mouse Actions

← Older revision		Revision as of 15:02, 25 April 2018
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	* ''Strg'' + ''left mouse button'': change type of nearest marker (with a different type) to 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		* ''Shift'' + ''left mouse button'': draw a closed region of interest, all markers inside the region are removed
			* ''Shift'' + ''Ctrl'' + ''left mouse button'': add a new marker (for a region) by drawing its contour

	=== Available Detectors ===		=== Available Detectors ===

Moeller: /* MTB Cell Counter */

2018-04-25T13:00:49Z

MTB Cell Counter

@@ Line 93: / Line 93: @@
 ** ''"Load Markers"'': loads markers from an XML file
 ** ''"Export Image"'': save a copy of the image including all markers
 ===== Keyboard Shortcuts and Mouse Actions =====
@@ Line 166: / Line 136: @@
 * ''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]

Moeller: /* MTB Cell Counter */

2018-04-25T12:59:28Z

MTB Cell Counter

← Older revision		Revision as of 14:59, 25 April 2018
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	** ''"Export Image"'': save a copy of the image including all markers		** ''"Export Image"'': save a copy of the image including all markers

	~~<br>~~		=== Available Detectors ===
			For detecting structures in the image the plugin provides a set of detectors which are described in more detail below.
			==== Particles with UWT ====
	[[File:ScreenshotConfigurationDetector.png\|350px\|right\|link=]]		[[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<br>		For the pre-segmentation of spot-like structures a particle detector operator of MiToBo is used. It has been published in<br>