LSM File Toolbox

Version (14.2 KB) by Peter Li
Functions for reading info databases of Zeiss LSM confocal microscope files.
Updated 18 Apr 2007

No License

Zeiss confocal microscopes output data in LSM files, a stacked TIFF image format with some additional headers and info directories. See for details. The functions included here will allow you to read the additional info, for example useful fields such as the pixel dimensions of the stack. I have based the current version heavily on the open source code from the LSM Toolbox plugin for ImageJ (

This toolbox does not read the actual image data from the file, for that you could simply export the images into simpler formats and then use IMREAD to import the data to MATLAB. There are also now versions of tiffread or other programs out there that can read the image data directly.

See comments for additional suggestions. Note also that if you have the .mdb file output by Zeiss, this is readable in Microsoft Access and includes much of the information available here.

Cite As

Peter Li (2024). LSM File Toolbox (, MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R13
Compatible with any release
Platform Compatibility
Windows macOS Linux
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Version Published Release Notes

Include acknowledgment of LSM Toolbox for ImageJ