Dissecting LSM files

From OpenWetWare
Jump to navigationJump to search

.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