Dissecting LSM files - Revision history

Jakob Suckale at 14:32, 16 December 2011

2011-12-16T14:32:58Z

←Older revision		Revision as of 14:32, 16 December 2011
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-	'''.LSM''' is Zeiss' proprietary image format based on [http://en.wikipedia.org/wiki/Tagged_Image_File_Format TIFF]. LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings. These can be viewed and extracted using additional tools like the ~~[http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start~~ LSM Toolbox] for ~~[http://fiji.sc~~ Fiji].	+	'''.LSM''' is Zeiss' proprietary image format based on [http://en.wikipedia.org/wiki/Tagged_Image_File_Format TIFF]. LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings. These can be viewed and extracted using additional tools like the LSM Toolbox for Fiji.

	== Imaging properties via a text editor ==		== Imaging properties via a text editor ==
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	</pre>		</pre>

		+	== Imaging properties via Fiji LSM Toolbox ==
		+
		+	Prerequisites
		+	* [http://fiji.sc Fiji] open access image software
		+	* [http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start LSM Toolbox] (screenshot below)
		+
		+	[[Image:Fiji LSM Toolbox.png]]

	== Links ==		== Links ==

2011-12-16T14:28:14Z

←Older revision		Revision as of 14:28, 16 December 2011
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	DimensionX = 1024		DimensionX = 1024
-
	DimensionY = 1024		DimensionY = 1024
-
	...		...
-
	ScalingX = 0.197 µm		ScalingX = 0.197 µm
-
	ScalingY = 0.197 µm		ScalingY = 0.197 µm
		+	...
		+	</pre>

		+	The interesting parameters come a few lines further down.
		+
		+	<pre>
		+	Objective = Plan-Apochromat 63x/1.4 Oil DIC
		+	...
		+	DetectorVoltage = 800.000 V
		+	...
		+	AmplifierOffset = 0.039
		+	...
		+	PinholeDiameter = 74.00 µm
	...		...
		+	Wavelength = 488.0 nm
		+	Transmission = 10.00 %
	</pre>		</pre>

2011-12-16T14:23:22Z

←Older revision		Revision as of 14:23, 16 December 2011
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	'''.LSM''' is Zeiss' proprietary image format based on [http://en.wikipedia.org/wiki/Tagged_Image_File_Format TIFF]. LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings. These can be viewed and extracted using additional tools like the [http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start LSM Toolbox] for [http://fiji.sc Fiji].		'''.LSM''' is Zeiss' proprietary image format based on [http://en.wikipedia.org/wiki/Tagged_Image_File_Format TIFF]. LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings. These can be viewed and extracted using additional tools like the [http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start LSM Toolbox] for [http://fiji.sc Fiji].
		+
		+	== Imaging properties via a text editor ==
		+
		+	One low tech method of checking the imaging settings is to open the LSM file in a text editor. The file starts with several hundreds of lines of partly illegible characters. In the files tested, imaging settings started at line 1652 with the following text:
		+
		+	<pre>
		+	BEGIN AcquisitionParameters 10002
		+
		+	DimensionX = 1024
		+
		+	DimensionY = 1024
		+
		+	...
		+
		+	ScalingX = 0.197 µm
		+
		+	ScalingY = 0.197 µm
		+
		+	...
		+	</pre>
		+

	== Links ==		== Links ==

2011-12-16T14:11:32Z

introduction

←Older revision		Revision as of 14:11, 16 December 2011
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		+	'''.LSM''' is Zeiss' proprietary image format based on [http://en.wikipedia.org/wiki/Tagged_Image_File_Format TIFF]. LSM files are the default data export for the Zeiss LSM series confocal microscopes (e.g. LSM 510, LSM 710). In addition to the image data, LSM files contain most imaging settings. These can be viewed and extracted using additional tools like the [http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start LSM Toolbox] for [http://fiji.sc Fiji].
		+
	== Links ==		== Links ==

2011-12-16T14:04:38Z

links

←Older revision		Revision as of 14:04, 16 December 2011
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	== Links ==		== Links ==

-	*	+	* [http://www.zeiss.de/LSM Zeiss LSM microscope page] (only the latest models) & [http://www.zeiss.de/lsm710 LSM 710 homepage]
		+	* [http://en.wikipedia.org/wiki/LSM_%28Zeiss%29 LSM entry wikipedia]
		+
		+	* [http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start Fiji LSM Toolbox] ([http://fiji.sc/wiki/index.php/Fiji Fiji] is an open source imaging package)
		+	* [http://www.mathworks.com/matlabcentral/fileexchange/8412-lsm-file-toolbox MatLab LSM toolbox]
		+
	* [[User:Etchevers/Notebook/Conference notes/2008/11/17\|Notes on LSM 510 Meta]]		* [[User:Etchevers/Notebook/Conference notes/2008/11/17\|Notes on LSM 510 Meta]]

2011-12-16T13:49:11Z

*** page created ***

←Older revision		Revision as of 13:49, 16 December 2011
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	*		*
-	* [[User:Etchevers/Notebook/Conference notes/2008/11/17 Notes on LSM 510 Meta]]	+	* [[User:Etchevers/Notebook/Conference notes/2008/11/17\|Notes on LSM 510 Meta]]

2011-12-16T13:42:01Z

links

New page

== Links ==

*
* [[User:Etchevers/Notebook/Conference notes/2008/11/17 Notes on LSM 510 Meta]]