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SPUTNIK (version 1.4.2)

Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit

Description

Set of tools for peak filtering of mass spectrometry imaging data based on spatial distribution of signal. Given a region-of-interest, representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimension and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimension and simplifying the chemical interpretation. The methods are described in Inglese P. et al (2019) .

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install.packages('SPUTNIK')

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327

Version

1.4.2

License

GPL (>= 3)

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Repository

https://github.com/paoloinglese/SPUTNIK

Maintainer

Paolo Inglese

Last Published

April 16th, 2024

Functions in SPUTNIK (1.4.2)

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.

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.

bladderMALDIRompp2010

Load the example MALDI-MSI data.

globalPeaksFilter

Reference similarity based peak selection.

Structural similarity index (SSIM).

normIntensity,msi.dataset-method

Normalize the peaks intensities.

Constructor for msi.dataset-class objects.

createPeaksFilter

Generate a peak filter object.

getIntensityMat,msi.dataset-method

Return the peaks intensity matrix.

applyPeaksFilter,msi.dataset-method

Apply the results of a peaks filter.

getMZ,msi.dataset-method

Return the m/z vector.

plot,ms.image,missing-method

Visualize an MS image. plot extends the generic function to ms.image-class objects.

Constructor for ms.image-class objects.

getShapeMSI,msi.dataset-method

Returns the geometrical shape of MSI dataset

msi.dataset-class

msi.dataset-class S4 class definition containing the information about the mass spectrometry imaging dataset.

removeSmallObjects,ms.image-method

Remove binary ROI objects smaller than user-defined number of pixels

Pixel scatteredness ratio.

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.

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.

binOtsu,ms.image-method

Binarize MS image using Otsu's thresholding.

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.

binKmeans,msi.dataset-method

Return a binary mask generated applying k-means clustering on first 10 principal components of peaks intensities.

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.

ms.image-class definition.

invertImage,ms.image-method

Invert the colors of an MS image.

Performs the peak selection based on complete spatial randomness test.

refImageBinaryOtsu

Calculate the binary reference image using Otsu's thresholding.

Normalized mutual information (NMI).

varTransform,msi.dataset-method

Variance stabilizing transformation.

closeImage,ms.image-method

Apply morphological closing to binary image.

countPixelsFilter

Filter based on the minimum number of connected pixels in the ROI.

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.

Spatial chaos measure.

smoothImage,ms.image-method

Apply Gaussian smoothing to an MS image.

ovarianDESIDoria2016

Load the example DESI-MSI data.

refImageContinuous

refImageContinuous returns the reference image, calculated using the method. This image represents the basic measure for the filters in SPUTNIK.

refImageBinarySVM

Calculate the binary reference image using linear SVM trained on manually selected pixels.