CSRPeaksFilter          Performs the peak selection based on complete
                        spatial randomness test.
NMI                     Normalized mutual information (NMI).
PCAImage,msi.dataset-method
                        Generates an RGB msImage representing the first
                        3 principal components. This image can be used
                        to qualitatively evaluate the spatial
                        heterogeneity of the sample.
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 first 10 principal components of
                        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.
numDetectedMSI,msi.dataset-method
                        Generates an msImage representing the number of
                        detected peaks per pixel. This image can be
                        used to qualitatively evaluate the spatial
                        heterogeneity of the sample.
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.
refImageBinaryKmeans    Calculate the binary reference image using
                        k-means clustering. K-Means is run on the first
                        'npcs' principal components to speed up the
                        calculations.
refImageBinaryKmeansMulti
                        Calculate the binary reference image using
                        k-means clustering with multi-cluster merging.
                        K-means is run on the first 'npcs' principal
                        components to speed up the calculations.
refImageBinaryOtsu      Calculate the binary reference image using
                        Otsu's thresholding.
refImageBinarySVM       Calculate the binary reference image using
                        linear SVM trained on manually selected pixels.
refImageContinuous      'refImageContinuous' returns the reference
                        image, calculated using the 'method'. This
                        image represents the basic measure for the
                        filters in SPUTNIK.
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.
totalIonCountMSI,msi.dataset-method
                        Generates an msImage representing pixels
                        total-ion-counts. This image can be used to
                        qualitatively evaluate the spatial
                        heterogeneity of the sample.
varTransform,msi.dataset-method
                        Variance stabilizing transformation.
