LSM (Zeiss)

"LSM" is a line of confocal laser scanning microscopes produced by the Zeiss company. As of 2005, the state of the art is the 5th generation, including the LSM 510, LSM 5 Pascal, and LSM 5 Live. The LSM 710 was released in 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.

File format details

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

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

* [http://www.zeiss.com/4125681F004CA025/Contents-Frame/C7B4C762D6F8A09A85256B4B0075CE56 Zeiss USA home for LSM products] includes a download for the free LSM Image Browser, a nice software for reading LSM file settings and exporting the image data (proprietary, closed source).
* [http://www.zeiss.com/sensitivity LSM 710] at Zeiss
* [http://rsb.info.nih.gov/ij/plugins/lsm-reader.html 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 [http://ibmp.u-strasbg.fr/sg/microscopie/methods/lsmio/os9/LSM_Read.java raw Java code] of a much earlier, out of date version.
* There is also an [http://ibb.gsf.de/homepage/karsten.rodenacker/IDL/FileIO.html IDL plugin] to read LSM 4.x and 5.x data file. From the webpage you even have access to the specification of [http://ibb.gsf.de/homepage/karsten.rodenacker/IDL/Lsmfile.doc File Format Description - LSM 5xx] .
* The Huygens Software in freeware mode can [http://support.svi.nl/wiki/FileFormats read and convert LSM files] .
* The free matlab function tiffread.m [http://www.cytosim.org/other] can import LSM image files into matlab.
* The open source python module pyLSM [https://launchpad.net/pylsm] gives the ability to open LSM images into python.