LSM (Zeiss)

LSM is a line of laser point scanning confocal and two photon microscopes produced by Carl Zeiss AG. The 5th generation, including the LSM 510, LSM 5 Pascal, and LSM 5 Live are now obsoleted by the LSM 700/710/780 series released after 2008.

LSM models produce a file format with the filename extension ".lsm". There are different generations of this file format depending on the generation of the microscope model, but all are essentially extensions of the TIFF multiple image stack file format, containing instrument specific hardware settings metadata and thumbnail images.

File format details

These are technical details intended for use by scientists trying to write code to read LSM files.

Carl Zeiss Microimaging can be contacted for a full file format description of the LSM 5/7 format.

At least in the 5th generation LSM format, important extensions to the normal TIFF format are:

1. An additional set of image directory entries (IFD entries are a standard part of the TIFF format that normally describe the individual images in a stack) starting at byte 8 of the file, after the standard TIFF header. This directory is mostly redundant with the standard TIFF image property directories that are included with the individual image data. One important special entry in this directory is the entry with tag code 34412, which provides the byte address within the file for an additional set of headers.
2. The additional set of headers pointed to by IFD entry 34412 includes more redundant information about the image files. More importantly, it includes byte address offsets for a number of important data blocks within the file.
3. One offset address provided in the additional headers is the location of the "scaninfo" directory. The scaninfo directory is a long series of entries organized in hierarchical subgroups providing most of the relevant settings used for the scanning run. The scaninfo directory is dynamic in length; it includes metadata entries that indicate what level of the hierarchy is being traversed. The end of the directory is reached when the metadata entries indicate traversal backwards past the "root" level of the hierarchy.

See external links below for code examples of reading LSM files.

External links

• Carl Zeiss downloads for LSM products includes a download for the free Zen LE 2009 and the old LSM Image Browser, for reading and browsing LSM file images and settings and also exporting the image data (proprietary, closed source).
• LSM 710 at Zeiss
• Bio-Formats: standalone open source Java library for reading and writing life sciences image file formats - used in ImageJ / Fiji, Open Microscopy Environment, etc.
• LSM-Reader is a plugin for the ImageJ program, an image processing toolkit written in Java and released by the NIH. If you want to see code examples for reading LSM files, check out the .jar file available here.
• If you cannot open the .jar file suggested above, here is the raw Java code of a much earlier, out of date version.
• There is also an IDL plugin to read LSM 4.x and 5.x data file. From the webpage you even have access to the specification of File Format Description - LSM 5xx.
• The Huygens Software in freeware mode can read and convert LSM files.
• The free matlab function tiffread.m [1] can import LSM image files into matlab.
• The open source python modules pyLSM [2] and tifffile.py [3] give the ability to open LSM images into python.
• Some LSM manipulation utilities written in C [4]