Some solutions to read lsm files: Under windows: ZEISS LSM image browser http://www.embl.de/eamnet/html/body_image_browser.html or http://www.zeiss.de/C12567BE0045ACF1/Contents-Frame/CAA2EF638EC5F0D3C1256ADF0050E2F1 Under linux: First install Wine http://www.winehq.org/download/ and then ZEISS LSM image browser Matlab toolbox: "The functions included here will allow you to read the additional info, for example useful fields such as the pixel dimensions of the stack. 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." http://www.mathworks.com/matlabcentral/fileexchange/8412