Dissecting LSM files

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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].  
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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 LSM Toolbox for Fiji.  
== Imaging properties via a text editor ==
== Imaging properties via a text editor ==
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DimensionX = 1024
DimensionX = 1024
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DimensionY = 1024
DimensionY = 1024
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         ...
         ...
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ScalingX = 0.197 µm
ScalingX = 0.197 µm
-
 
ScalingY = 0.197 µm
ScalingY = 0.197 µm
 +
        ...
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</pre>
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The interesting parameters come a few lines further down.
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<pre>
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Objective = Plan-Apochromat 63x/1.4 Oil DIC
         ...
         ...
 +
DetectorVoltage = 800.000 V
 +
        ...
 +
AmplifierOffset = 0.039
 +
        ...
 +
PinholeDiameter = 74.00 µm
 +
        ...
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Wavelength = 488.0 nm
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Transmission = 10.00 %
</pre>
</pre>
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== Imaging properties via Fiji LSM Toolbox ==
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Prerequisites
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* [http://fiji.sc Fiji] open access image software
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* [http://imagejdocu.tudor.lu/doku.php?id=plugin:inputoutput:lsmtoolbox:start LSM Toolbox] (screenshot below)
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[[Image:Fiji LSM Toolbox.png]]
== Links ==
== Links ==

Current revision

.LSM is Zeiss' proprietary image format based on 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

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:

BEGIN AcquisitionParameters 10002

	DimensionX = 1024
	DimensionY = 1024
        ...
	ScalingX = 0.197 µm
	ScalingY = 0.197 µm
        ...

The interesting parameters come a few lines further down.

	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 %

Imaging properties via Fiji LSM Toolbox

Prerequisites

Image:Fiji LSM Toolbox.png

Links

Personal tools