Look@NanoSIMS (abbreviated as LANS) is a free software for the analysis of NanoSIMS image data produced by the Cameca NanoSIMS 50L instrument. It is distributed as a Matlab code, thus requires Matlab (proprietary software) installed on your system to run.

• Loading of secondary ion counts (SIC) image data (Cameca *.im files)
  • all planes and masses (default)
  • in blocks
  • selected planes and masses
  • merging of multiple *.im files into one
  • dead-time and QSA corrections applicable
  • support of zip-compressed input data (*.im.zip files)
  • Matlab files (*.mat) produced by processing with LANS, without the need of the original *.im file. (Because this loads drift-corrected and accumulated data for each SIC image, analysis of depth profiles is not possible in this case.)
• Accumulation of planes, with drift-correction applied
• Definition of regions of interest (ROIs)
  • manual and semi-automated
  • based on NanoSIMS images, or on an imported external image (e.g., FISH, TEM, SEM, AFM) with alignment done within LANS
  • ROI classification (manual & automated based on a logical expression)
  • watershed segmentation of ROIs
• Quantification of isotopic and elemental ratios (defined through an arbitrary expression)
• Display and export of results in text and graphics formats
  • images (various colormaps, ROI outlines can be included, hue intensity can be modulated)
  • lateral and depth profiles
  • histograms
  • scatter plots (color-coded based on ROI classification)
  • overlays of nanoSIMS images in an RGB image
  • overlays of nanoSIMS and external images in an RGB image or a 3D surface plot
• Statistical analysis of data in ROIs
  • comparison of ROIs
  • comparison of ROI classes
  • comparison of treatments or experimental time-points
• Tools for processing and statistical analysis of multiple nanoSIMS datasets
  • images
  • interactive scatter plots
  • statistical comparison of ROIs, ROI classes and treatments
  • depth profiles in ROIs
  • automated reprocessing of previously processed datasets

• Install Matlab. You will need the core Matlab and the image processing and statistical toolboxes. Presently, LANS requires Matlab 2013b. The use of a newer Matlab version is not recommended because some of the features introduced by the release of Matlab 2014a (a major overhaul of graphics) have not been fully implemented/updated in LANS.
• Install LaTeX. This is required to support export of graphical output as tagged PDF documents.
  • required executables: epstopdf and pdflatex
  • required packages graphicx, geometry and hyperref
  • use LaTeX distributions: TeX live package (Linux), MikTeX (Windows), MacTex (MacOS)
• Install a program for decompressing zip files
  • 7-Zip (freeware) is recommended for Windows.
  • Linux and MacOS systems have it by default (unzip).
• Download the latest stable version of LANS from this Dropbox folder, and unzip it in a folder of your choice.

Before running LANS for the first time, it is recommended to read carefully the files lookatnanosims.m and paths.m to check system-specific settings.

Start Matlab and set Matlab's working directory to the folder where you unzipped LANS. In the Matlab console, type pwd and then ls, both followed by pressing the Enter key, to check that you are in the correct directory and to ensure that the file lookatnanosims.m is present. Finally, type lookatnanosims and press the Enter key. That's it. This should start the graphical user interface (GUI) of the LANS program.

Please include the following citation if you used LANS in your work.

L. Polerecky, B. Adam, J. Milucka, N. Musat, T. Vagner, M. M. M. Kuypers (2012). Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology. Environmental Microbiology 14 (4): 1009–1023 (doi:10.1111/j.1462-2920.2011.02681.x)

Note that LANS is under continuous development, with bugs fixed and new features added every couple of months. This costs a lot of time, effort and energy. Thus, a little extra "thanks to LP" in the acknowledgement section of your paper will be highly appreciated and motivating.

E-mail the main developer (LP) if you experience problems, or if you would like to have new features added to, or participate in the development of, the program.