Organization of the input and output data

To facilitate efficient data processing, especially through the metafile processing function, datasets belonging to a given experiment, including the raw image stack files (files with extension im) and the information files (files with extension chk im), need to be copied to a single directory (Fig. 2A). The names of the directory and dataset files must not contain spaces. The processed information for a given dataset is stored in a directory of the same name as the input file name. This directory is further structured into sub-directories that contain exported information in the Matlab (mat), vector graphics (eps and pdf), bitmap (tif) and text (dat, tests and tex) formats (Fig. 2B).

Input data format

Each dataset must comprise two files, (i) the raw image stack (file with extension im) and (ii) the information file (extension chk im). The first file contains the detected ion counts stored in a binary format, whereas the second file contains information about the structure of the binary file (names and masses of the detected ions, raster size, stage position, etc.; Fig. 3). This information is essential for the Look@NanoSIMS program to correctly load the binary file. Make sure with the operator of the Nanosims instrument that this file is generated for each measurement.