Schematic outlining the IVEN pipeline (MATLAB).

Data from IMARIS (or equivalent segmentation program) are output as an Excel file and compiled as outlined in tutorials in order to ensure that all data are imported correctly into IVEN (yellow box). Files are then selected using the standard file browser window (grey box). The embryo schematic and original cell classifications are generated and displayed to allow for user correction of the automatic cell classification (blue boxes). Channel intensities can be used to assist in correction of the cell classification if analysing confocal images. Method of thresholding of the DT is then chosen by the user, with a variety of options and tunable parameters (green box). After analysis, an output of thresholds used and number of cells analysed is output to the command window (orange box). Finally, an Excel file with all original input data as well as the numbers of neighbours and neighbourhood compositions is output, along with the embryo schematic with final cell classifications (purple boxes). DT, Delaunay triangulation; IVEN, Internal Versus External Neighbourhood.

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