LSM Toolbox
© 2008 Patrick Pirrotte
Description The LSM Toolbox opens Zeiss Laser Scanning Microsope (confocal microscopes) and extracts acquisition information. The actual version of the LSM Toolbox is a complete rewrite of the previous LSM_Reader ImageJ plugin. On most platforms the reading speed should noticeably be improved. Since version 4.0 the LSM_Reader has been split into two subprojects,
  • the LSM_Toolbox, the complete toolbox, which will hopefully continue evolve into a fully fledged ImageJ extension for the manipulation of Zeiss LSM images.
  • the LSM_Reader proper which is a simple reader integrated into the standard distribution of ImageJ.
The LSM Reader is based on a cut down version of the LSM Toolbox and lacks many features of the toolbox plugin.

Authors

  • Patrick Pirrotte (project maintainer, patrick@image-archive.org)
  • Jérôme Mutterer (jerome.mutterer@ibmp-ulp.u-strasbg.fr)

Code contribution and bug reports:

For bugs, code contributions or wishes, contact Patrick (patrick@image-archive.org). Several features of LSM Toolbox are somewhat experimental and may yield unexpected results. The preview features in the JFileChooser dialog (Open LSM command) only shows the first thumbnail of the first channel to avoid reading the whole file. On an Intel 2.4 Ghz 1GB RAM computer running Windows XP this is pretty fast.

Compatibilty and requirements:

Tested under Sun Java Runtime Engine JRE 1.4.2.09 and 1.5.06 in ImageJ v1.35 onward.

Opens Zeiss image files using the ImageJ framework. The LSM_Reader plugin uses HyperVolume_Browser (>=v1.1) [1] and/or Image5D (>=v1.1.6) [2] for timelapse or spectral image representation if present. The presence of LUT_Panel (v2.2) [3] allows channel recoloring. Moreover, LSM_Fusion [4] and LSM_Merge [5] are supported if present.

Acknowledgments:

Previous versions (up to v3.2b) were developped at the Institut de Biologie Moleculaire des Plantes (Strasbourg, France), first by Yannick Krempp (up to v2.2), then by Patrick Pirrotte (since v2.2). During all these years, Jérôme Mutterer has been one to test test and test again, suggesting numerous improvments and fixing some of the bugs. The plugin would not have been made possible without the help of Zeiss, which is not affiliated to this project besides helping us understand the tricky lsm format. Thank you to all the other contributors who helped us debug the LSM_Reader and the LSM Toolbox, especially Wayne Rasband (wayne@codon.nih.gov).

[1] HyperVolume_Browser, Patrick Pirrotte and Jérôme Mutterer, available at http://rsb.info.nih.gov/ij and http://www.image-archive.org
[2] Image5D, Joachim Walter, available at http://rsb.info.nih.gov/ij
[3] Lut_Panel, Patrick Pirrotte and Jérôme Mutterer, available at http://rsb.info.nih.gov/ij and http://www.image-archive.org
[4] LSM_Merge, Jérôme Mutterer, available at http://rsb.info.nih.gov/ij
[5] LSM_Fusion, Jérôme Mutterer, available at http://rsb.info.nih.gov/ij