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LSM File Toolbox

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LSM File Toolbox

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31 Aug 2005 (Updated )

Functions for reading info databases of Zeiss LSM confocal microscope files.

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Description

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.

Acknowledgements

This file inspired Zeiss Laser Scanning Confocal Microscope Lsm File Reader.

MATLAB release MATLAB 6.5 (R13)
Other requirements Included is both the LSM toolbox, and my CStruct toolbox, which provides generalized methods for reading structured data from files. CStruct is required by LSM. Not the same as the other CStruct toolbox available on FileExchange!
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Comments and Ratings (11)
22 Nov 2011 Kristin

lsminfo worked out of the box for me. thanks!

09 Nov 2011 Diego Pacheco  
09 Nov 2011 Diego Pacheco

Hi Arthur, I did a time series scan, with a marker using trigger in 1, and I could not find any variable that provide me the time at which this events happened (markers). would you tell me if there is a vector or cell that provides this information?

Thanks

26 Aug 2011 Peter Li

Thanks Arthur, I probably will not get around to looking into this for a long time but hopefully your comment will help people avoid any trouble.

01 Jun 2011 Bhavna Rajasekaran

Brilliant, thank you! What exactly I was looking for

06 Apr 2011 Arthur

I noticed a small bug in reading the scaninfo. The last character of all strings were chopped off. In scaninforead.m I changed line 46 to

value = value(1:end-1);

which solved it for me.

21 Dec 2010 Arthur

Very usefull tool

28 Feb 2010 Anton Semechko

To read in the CLSM slice directly into MatLab download m-file called tiffread.m

Google search it or get the m-code here:
http://www.cytosim.org/other/tiffread.m

09 Feb 2006 norbert kirchgessner

very nice tool to get all info of lsm data
lsminfo spends most of its time with imfinfo, can be commented out..

01 Nov 2005 Andrew Chen

wait I should supply a link for tiffread

http://www.cytosim.org/other/

thanks Peter Li!

01 Nov 2005 Andrew Chen

Very useful for me. Saves me some headaches of making text files for matlab to read.

I want to let yalls know that some folks wrote 'tiffread.m' and the 4th version of it can read images, but make sure that your lsm files are saved with no palette.

Updates
26 Sep 2005

Trying to fix hyperlink, clarifying that CStruct is required.

24 Mar 2006

Additional suggestions and cleaning up HTML problem

08 Nov 2006

Information about other code that can be used in conjunction with my work.

16 Apr 2007

More fields are now read. Outputs are simplified: a single struct is returned with additional data in substructs. Despite changes, should remain be backward compatible except for very unusual cases, covered in the file comments.

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