GeoLab – centralized lab facility at the Faculty of Geosciences

GeoLab – centralized lab facility at the Faculty of Geosciences

Look@NanoSIMS software

Look@NanoSIMS (abbreviated as LANS) is a free software for the analysis of NanoSIMS image data produced by the Cameca NanoSIMS 50L instrument (read more on LANS in Polerecky et al., 2012). It is distributed as a Matlab code, thus requires Matlab (proprietary software) installed on your system to run.

For the users of our NanoSIMS facility, LANS is provided on a dedicated computer available in the NanoSIMS Lab. In addition to our collaborators, we recommend to everybody to analyse their NanoSIMS data.

Please contact us in case you experience problems with LANS or if you would like to have new features added to the software.

We continuously improve the LANS software, the most recent version of LANS is 2022-09-02.

1. 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.)
2. Accumulation of planes, with drift-correction applied
3. 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
4. Quantification of isotopic and elemental ratios (defined through an arbitrary expression)
5. 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
6. Statistical analysis of data in ROIs
  • comparison of ROIs
  • comparison of ROI classes
  • comparison of treatments or experimental time-points
7. 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

Download the latest stable version of LANS, including program, manual and test-data from the LANS Dropbox folder.

Although it is rather outdated (written in 2011), the manual is the best starting point for you to learn about LANS. Once you have learned about the basic approaches described there, you will more easily understand the description of new features given below.

1. Installing LANS
  • Install Matlab. You will need the core Matlab and the image processing and statistical toolboxes. Presently, LANS requires Matlab 2019b or newer.

  • Install LaTeX. This is required to support export of graphical output as tagged PDF documents.

    • use well-known LaTeX distributions: TeX live package (Linux), MikTeX (Windows), MacTex (MacOS)

    • required executables: epstopdf and pdflatex

    • required LaTeX packages: graphicx, geometry and hyperref

  • Install a program for decompressing zip files

    • 7-Zip (freeware) is recommended for Windows.

    • unzip is available by default on Linux and MacOS systems

  • Download LANS as described above, and unzip it to a folder of your choice. Proceed as described below.
2. Running LANS
  • 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, as shown below.

  • Finally, type lookatnanosims and press Enter. That’s it. This should start the graphical user interface (GUI) of the LANS program shown below.

Help available via LANS‘s GUI
    Tooltips and extra help were added in several places of the LANS‘s GUI. Just hold your mouse above a specific checkbox or text field, or select a specific item from the newly added help menus, to display this extra help.
Default filename for ROIs file
    Because LANS was originally developed for microbiologists, the default name for the file containing the information about the regions of interest (ROIs) was cells. In the newest version the default filename can be chosen by the user by specifying the value of the global variable CELLSFILE, which is done by editing the lookatnanosims.m file in the root of the LANS distribution.
    A possible, and perhaps more appropriate, default filename could be ROIs. Note that because the ROI files are used during post-processing of multiple files, it is recommended to consistently use one filename throughout your LANS analyses.
Analysis of zip-compressed *.im files
    The *.im files produced by the NanoSIMS instrument are usually quite large, which may not be convenient if your disk space is limited or if you store and analyze them on different computers and thus need to copy them over the network. To make the raw data storage more efficient, it is recommended to compress the *.im files as zip files (*.im.zip). To do this, you can use the 7-Zip program, which is a freeware software for Windows, or the zip program, which is by default available on Linux and Mac-OS systems. Once this is done, LANS allows you to analyze these compressed data as well. To make this possible you need to edit the file paths.m present in the root folder of your LANS distribution and specify the full path of the decompressing (“unzipping”) command in the UNZIP_COMMAND variable. Subsequently, when loading the raw dataset in LANS, select Compressed Cameca IM file (*.im.zip) as the File Type and then select your im.zip file. The data will be automatically decompressed and loaded into LANS, and you won’t need to worry about the large *.im files any more.
last-column/last-row bug of *.im files
    When processing an *.im file, you may have noticed that the images have a strange artifact. Specifically, it seems that the upper-most row and the left-most column of the image are not where they should be, but are instead in the lower-most and right-most parts of the image, respectively. Apparently, this is an issue related to the synchronization of primary and secondary ion beams in the NanoSIMS instrument, and is a technical problem that needs to be dealt with by Cameca. Since this has not happened so far, LANS implements a workaround to deal with this issue:
    Before loading the binary *.im file, check one or more of the options in the Input → Shift columns or rows when loading raw data. If you check more than one, the selected corrections will be done in the order from top to bottom. Then proceed with loading the file via Input → Load RAW dataset. You will see a notification that this correction was applied to the raw data in the Matlab console. Process the file the usual way. At the end, make sure you have these options checked when saving the preferences, so that you don’t need to worry about this correction when loading the file next time via Input → Load+accumulate+display RAW or PROCESSED dataset.
Diverse colormaps can be selected in additional output options
    It is possible to select from a more diverse range of colormaps when displaying images. To do this, select Preferences → Additional output options. In the window that pops up select the colormap of your choice from the pop-up menu, and click Apply. From this moment the selected colormap will be applied to (most of) the images displayed. Note that checking B/W in the main LANS GUI next to the scale field will override this choice and lead to the image displayed using the gray-scale colormap.
Loading accumulated data without the original binary *.im file
    It is possible to load the NanoSIMS data previously processed by LANS without the need for the original *.im binary data. To do so, select Load ACCUMULATED data from the Input menu of LANS, and select the preferences file (e.g., prefs.mat) that you saved during the time when you processed the original data with LANS. Based on the information in this file, the accumulated ion count images (*.mat files) will be loaded from the mat subfolder containing the processed data, after which you can proceed with the analysis of the data in the usual way. Note that when loading data in this way, LANS functions dealing with depth profiles will not be possible since the loaded dataset consists effectively only of one plane.
Quick scaling of mass and ratio images
    To produce printer-ready images of secondary ion counts or their ratios in an EPS, PDF or TIF format, you need to display the images through Output → Display masses or Output → Display ratios while the Export PDF graphics option is checked. However, to optimize the appearance, you will likely need to adjust the scale in which the images are displayed. To do this quickly, type the minimum and maximum values in the corresponding scale fields and press Enter. For example, if you want display the 13C/12C ratio in the scale from 0.007 to 0.02, type [0.007 0.02] in the scale field. If you want to display the image auto-scaled, type [auto] in the corresponding scale field. Auto-scaling is then done based on the quantiles specified via Preferences → Additional output options. Note that in the Additional output options window you can also select the color map of the image. At the very end, when satisfied with the outcome, do not forget to export the results through Output → Display masses or Output → Display ratios.

If you find a bug in the LANS software, please report it to us so we can fix it. When reporting a bug, please include the following files:

  • a screenshot of your LANS Matlab session
  • the text of the error-message
  • the raw data (*.im file) for which the error occurred
  • the zipped folder that contains all the output (most notably the files prefs.mat, xyalign.mat, cells.mat, cells.dat) that you have generated from the data until the error occurred.

Please compress those files into one zip file and send it to Lubos Polerecky using an on-line file transfer service (e.g., www.wetransfer.com). Please do not send this information directly by e-mail, as the file will likely be too large.

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