LSM Reader

Authors: Patrick Pirrotte (patrick at
Yannick Krempp (yannick.krempp at
Jerome Mutterer (jerome.mutterer at
Source:Contained in LSM_Reader.jar, which can be opened using a ZIP utility
Installation: This plugin is included with ImageJ 1.36 and later. Download LSM_Reader.jar to the plugins folder to upgrade to the latest version. An earlier version (LSM_Reader v1.40) is also available. This version does not open files as hyperstack and it works with ImageJ 1.38 and earlier.
Description: This plugin reads *.lsm files produced by Zeiss LSM 510 confocal microscopes. Each channel of an image plane, stack, lambda or time serie is opened as a separate image or stack window. It is also available on the ImageJ Documentation Wiki. It is a cut-down version of the LSM Toolbox, which contains many more features: complete extraction of all metadata, time events, lambda and time stamps, etc.
See Also: LSM Toolbox plugin
LSM Batch With Colors macro
History: 2002/07/16 (v1.1): First released version
2002/09/16 (v1.2): Fixes a bug that prevented the opening of specific images containing textual notes together with single channel fluorescence data.
2003/01/23 (v2.2): Handles 12 bits datasets and timelapse datasets. Single image info window.
2003/05/12 (v3.2): Handles all uncompressed image files acquired with version up to 3.2 of the manufacturer's software (eg. xyz.lambda.time series). Channels acquisition colors preserved. Image stamping for depth, time, lambda. Full acquisition informations available through a Jtree categorized info viewer. Direct links to palette editor LUT_Panel and 4D navigator HyperVolume_Browser plugins if installed.
2003/07/15 (v3.2b): Bug in reading 12 bit data fixed. Stamps can now be applied on the images or dumpped to a text window for further custom usage.
2003/05/12 (v3.2d): Adds "Batch Convert" function. Works with the "Handle Extra File Types" plugin.
2004/01/06: Packaged as JAR file that includes "LSM Channels Merge" and "LSM Files Fusion" plugins.
2005/07/19 (v3.2e): Works with ImageJ 1.34.
2005/09/19 (v3.2f): Works with macros.
2006/10/16 (v4.0): Faster. Opens compressed images. Compatible with the latest LSM file format.
2008/04/08 (v4.0c): Opens files as hyperstacks. Requires ImageJ 1.39 or later.
2008/04/22 (v4.0d): Fixes a bug that caused an exception when opening linescans.
2009/07/01 (v4.0f): Added support for point-scans and fixed LZW-related bug.
2011/04/04 (v4.0g): Fixes a bug that caused an exception when opening multiposition stacks.

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