LSM File Toolbox
Updated 18 Apr 2007
Zeiss confocal microscopes output data in LSM files, a stacked TIFF image format with some additional headers and info directories. See http://en.wikipedia.org/wiki/LSM_(Zeiss) 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 (http://imagejdocu.tudor.lu/Members/ppirrotte/lsmtoolbox).
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.
Peter Li (2023). LSM File Toolbox (https://www.mathworks.com/matlabcentral/fileexchange/8412-lsm-file-toolbox), MATLAB Central File Exchange. Retrieved .
MATLAB Release Compatibility
Platform CompatibilityWindows macOS Linux
Inspired: Zeiss Laser Scanning Confocal Microscope LSM file reader, 3D blob segmentation
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