Dissecting LSM files

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(links)
Current revision (09:32, 16 December 2011) (view source)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
 +
'''.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 ==
 +
 +
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>
 +
 +
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>
 +
 +
== 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 ==
-
*  
+
* [http://www.zeiss.de/LSM Zeiss LSM microscope page] (only the latest models) & [http://www.zeiss.de/lsm710 LSM 710 homepage]
-
* [[User:Etchevers/Notebook/Conference notes/2008/11/17 Notes on LSM 510 Meta]]
+
* [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]]

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