Man pages for prafols/rMSI
MSI Tools

AppendNormalizationCoefsAppendNormalizationCoefs: Appends a new normalization...
AverageSpectrumAverageSpectrum. Computes the average spectrum of a whole...
BaseSpectrumBaseSpectrum. Computes the base spectrum of a whole rMSI...
builRasterImageFromColsBuild a image slice from specified datacube columns.
builRasterImageFromMassBuild a image slice from specified datacube masses.
ConvertBin2rMSIimgConvertBin2rMSIimg.
ConvertrMSIimg2BinConvertrMSIimg2Bin.
CountImagesInBrukerXmlCountImagesInBrukerXml.
CreateEmptyImageCreate an empty rMSI object with defined mass axis and size.
CreateSubDatasetCreateSubDataset.
DeleteRamdiskRemove an rMSI object ramdisk
getCoordsFromIdsgetCoordsFromIds Obtain images coords from a set of Ids.
getCubeRowFromCoordsObtain the cube index and cube row of a given image coords.
getCubeRowFromIdsObtain the cube index and cube row of a given image Ids.
getIdsFromCoordsObtain the image Identifiers from a given set of images...
getImageColsFromMassObtain the rMSI datacube columns corresponding to a mass.
importBrukerXmassImgImport a MSI dataset from Bruker XMASS folder and a XML file.
importBrukerXMASSImg_WizardImport a MSI dataset from Bruker XMASS folder and a XML file...
import_imzMLimport_imzML.
import_rMSItarimport_rMSItar.
imzMLparseimzMLparse. Parses a imzML file and obtain all relevant data...
insertRasterImageAtColsInserts a image at specified Cols of a rMSI object.
insertRasterImageAtMassInserts a image at specified mass of a rMSI object.
loadImageSliceFromColsLoad a image slice from a specified datacube columns.
loadImageSliceFromMassLoad a image slice from a specified mass and tolerance.
loadImgChunkFromCoordsLoads a part of a ff data img in RAM.
loadImgChunkFromCubeLoads a part of a ff data img in RAM.
loadImgChunkFromIdsLoads a part of a ff data img in RAM.
LoadMsiDataLoad rMSI data from a compressed tar.
MergeMassAxisMergeMassAxis.
MSIWindowOpen the GUI to explore a MS image
NormalizeByAcqDegradationNormalizeByAcqDegradation: Normalizes an rMSI image to...
NormalizeByAcqDegradationOnTargetPeaksNormalizeByAcqDegradationOnTargetPeaks: Calculates the...
NormalizeMAXNormalizeMAX: Calculates the MAX normalizatin of each pixel...
NormalizeRMSNormalizeRMS: Calculates the RMS normalizatin of each pixel...
NormalizeTargetPeaksNormalizeTargetPeaks: Calculates the normalization of each...
NormalizeTICNormalizeTIC: Calculates the TIC normalizatin of each pixel...
OpenMSIOpen a MS image from Hdd directly allowing the user to chose...
ParseBrukerXMLParseBrukerXML.
PlotClusterImagePlotClusterImage. Plot a segmentation image with the...
plotMassImageByPeakPlot a mass image of a up to 3 selected ions.
plotParamAcqOrderedplotParamAcqOrdered.
plotRGBDataOnImgplotRGBDataOnImg: Function to plot generic data on a RGB...
plotSpectraPlot Mass Spectra in a interactive way.
PlotTICImagePlotTICImage.
PlotValuesPlotValues.
plotVariousMassImagesByPeakPlots a image using various MS image objects and the same...
ReadBrukerRoiXMLReadBrukerRoiXML.
remap2ImageCoordsremap2ImageCoords.
saveImageSliceAtColsOverwrite an image slice of an rMSI object.
saveImageSliceAtMassOverwrite an image slice of an rMSI object.
saveImgChunkAtCoordsStores a data matrix to a part of ff data img.
saveImgChunkAtIdsStores a data matrix to a part of ff data img.
saveImgChunkToCubeSave a data matrix to a whole cube in rMSI object
SaveMsiDataSave a rMSI object to disk in a compressed .tar file.
SortIDsByAcquisitionSortIDsByAcquisition: Order the rMSI pixel IDs according the...
xmlParseSpectraxmlParseSpectra.
xmlParseSpectrumxmlParseSpectrum.
prafols/rMSI documentation built on Sept. 20, 2017, 2:58 p.m.