Look@NanoSIMS (abbreviated as LANS) is a free software for the analysis of NanoSIMS image data acquired by the Cameca NanoSIMS 50L instrument. It is distributed as a Matlab code, thus it requires a working installation of Matlab (proprietary software) to run.

The software is written and maintained by Lubos Polerecky (LP). The development started in 2008, at the time when LP worked at the Max-Planck Institute for Marine Microbiology in Bremen, Germany. Since 2013, LP continues with the development of the program as part of his permanent employment at Utrecht University in the Netherlands.

Although LANS has matured pretty well over the years, it may still contain bugs or lack features that you might find useful. If you experience problems, find a bug, or would like to have a new feature added to LANS, you can contact LP via email - he will be happy to work with you to fix them and improve the program. Contact detail: l (dot) polerecky (at) uu (dot) nl

Current version: 2023-06-09

1. Loading of secondary ion counts (SIC) image data (Cameca im files)

   • all planes and masses (default)
   • selected planes and masses
   • planes in blocks
   • merging multiple im files into one dataset
   • corrections for dead-time and QSA
   • compressed data (im.zip files, roughly 10% size of the original im files)
   • data previously processed and exported by LANS (mat)

2. Drift-correction and accumulation of planes

   • based on a specific mass and area within the image

3. Regions of interest (ROIs)

   • manual and semi-automated ROI definition
   • manual and semi-automated ROI classification (e.g., based on a logical expression)

4. Quantification and export of isotope and element ratios

   • ratios defined through an expression (e.g., 13C/12C, 13C/(12C+13C))
   • scatter plots of ROI-specific ratios (color-coded based on ROI classification)
   • ratio images (various colormaps, ROI outlines can be included, hue intensity can be modulated)
   • lateral and depth profiles (incl. depth variation of a lateral profile)
   • histograms
   • image overlays (combined into an RGB image or a 3D surface plot)
   • results exported as text and graphics

5. Statistical analysis of data in ROIs

   • comparison of ROIs
   • comparison of ROI classes
   • comparison of treatments or experimental time-points

6. Processing of multiple nanoSIMS datasets (aka "metafile processing")

   • scatter plots (interactive)
   • images and image overlays
   • statistical analysis of ROIs, ROI classes, and treatments
   • depth profiles in ROIs
   • automated reprocessing of previously processed datasets

7. Import of external (third-party) images (e.g., TEM, SEM, AFM, fluorescence)

   • image alignment done within LANS

LANS manuals are available from this Dropbox folder.

Although the original manual (LANS-manual.pdf) is rather outdated (written in 2011), it is the best starting point for you to learn about LANS. Once you have learned about the basic approaches described there, you can proceed by reading about extra features and functions described in LANS-extras.pdf.

• For convenience, the compressed file containing the latest version of LANS is stored in this Dropbox folder. Click on the program folder and then select the file LANS-latest-src.zip.
• If you are already using LANS and want to update it to the newest version, enter lans_webupdate in Matlab console.
• Of course, you can download LANS from the folder src in this repository.

1. Install Matlab.

   • You will need the core Matlab and the image processing and statistics and machine learning toolboxes.
   • Presently, LANS requires Matlab 2019b or newer.

2. Install LaTeX.

   • This software is required to enable export of graphical output as tagged PDF documents.
   • Use one of the well-known LaTeX distributions for your operating system, e.g., texlive (Linux), MikTeX (Windows), MacTex (MacOS).
   • required executables: epstopdf, pdflatex
   • required LaTeX packages: graphicx, geometry, hyperref

3. Install software for decompressing zip files.

   • This software is required to enable loading of compressed datasets (im.zip files). This is a useful feature because im.zip files have roughly a 10-fold lower size than the original im files.
   • 7-Zip (freeware) is recommended for Windows.
   • unzip is available by default on Linux and MacOS systems.

4. Install and run LANS

   • Download LANS as described above.
   • Unzip LANS-latest-src.zip to a folder of your choice.
   • Start Matlab and set the current folder to the LANS folder.
   • Enter lookatnanosims in Matlab console. This should open the main LANS graphical user interface, as shown below. You can start from there, as explained in the manuals.

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