Dissecting LSM files

.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

• Fiji open access image software
• LSM Toolbox (screenshot below)

Links

• Zeiss LSM microscope page (only the latest models) & LSM 710 homepage
• LSM entry wikipedia

• Fiji LSM Toolbox (Fiji is an open source imaging package)
• MatLab LSM toolbox

• Notes on LSM 510 Meta