CSRPeaksFilter          Performs the peak selection based on complete
                        spatial randomness test.
NMI                     Normalized mutual information (NMI).
SSIM                    Structural similarity index (SSIM).
applyPeaksFilter,msi.dataset-method
                        Apply the results of a peaks filter.
binKmeans,msi.dataset-method
                        Return a binary mask generated applying k-means
                        clustering on peaks intensities.
binKmeans2,msi.dataset-method
                        Return a binary mask generated applying k-means
                        clustering on peaks intensities. A finer
                        segmentation is obtained by using a larger
                        number of clusters than 2. The off-sample
                        clusters are merged looking at the most
                        frequent labels in the image corners. The
                        lookup areas are defined by the kernel size.
binOtsu,ms.image-method
                        Binarize MS image using Otsu's thresholding.
binSupervised,msi.dataset-method
                        Return a binary mask generated applying a
                        supervised classifier on peaks intensities
                        using manually selected regions corresponding
                        to off-sample and sample-related areas.
bladderMALDIRompp2010   Load the example MALDI-MSI data.
closeImage,ms.image-method
                        Apply morphological closing to binary image.
countPixelsFilter       Filter based on the minimum number of connected
                        pixels in the ROI.
createPeaksFilter       Generate a peak filter object.
getIntensityMat,msi.dataset-method
                        Return the peaks intensity matrix.
getMZ,msi.dataset-method
                        Return the m/z vector.
getShapeMSI,msi.dataset-method
                        Returns the geometrical shape of MSI dataset
gini.index              Gini index.
globalPeaksFilter       Reference similarity based peak selection.
invertImage,ms.image-method
                        Invert the colors of an MS image.
ms.image-class          ms.image-class definition.
msImage                 Constructor for ms.image-class objects.
msi.dataset-class       msi.dataset-class S4 class definition
                        containing the information about the mass
                        spectrometry imaging dataset.
msiDataset              Constructor for msi.dataset-class objects.
normIntensity,msi.dataset-method
                        Normalize the peaks intensities.
ovarianDESIDoria2016    Load the example DESI-MSI data.
plot,ms.image,missing-method
                        Visualize an MS image. 'plot' extends the
                        generic function to ms.image-class objects.
refAndROIimages         Compute the reference image and the ROI mask.
removeSmallObjects,ms.image-method
                        Remove binary ROI objects smaller than
                        user-defined number of pixels
scatter.ratio           Pixel scatteredness ratio.
smoothImage,ms.image-method
                        Apply Gaussian smoothing to an MS image.
spatial.chaos           Spatial chaos measure.
splitPeaksFilter        Test for the presence of split peaks.
varTransform,msi.dataset-method
                        Variance stabilizing transformation.
