importBrukerXmassImg: Import a MSI dataset from Bruker XMASS folder and a XML file.

In prafols/rMSI: MSI Tools

Description

This function converts MSI data contained in Bruker XMASS directory into rMSI data structure. Only spectra contained in the XML file are imported. The ramdisk will be created at the specified directory as a collection of ff files with the maximum specified size (50 MB is the default setting). The rMSI object pointing to ramdisk and containing RAM stored variables is returned.

Usage

importBrukerXmassImg(
  raw_data_full_path,
  resolution_um,
  xml_file_full_path,
  txt_spectrum_path = NULL,
  selected_img = 1,
  ...
)

Arguments

raw_data_full_path	Where the Bruker XMASS data is located.
resolution_um	The image pixel size un micrometers (sorry it can not be read directly from XMASS).
xml_file_full_path	Full path to the XML file or alternatively an already parsed xml list resulting from ParseBrukerXML() function.
txt_spectrum_path	Full path to a bruker spectrum txt file to extract mass axis (optional).
selected_img	the image number to select in the XML file containing various classes.
...	Extra parameters to .readBrukerXmassImg ( for example max_ff_file_size_MB as max size in MB of each ff file of the ramdisk).

prafols/rMSI documentation built on Dec. 12, 2021, 7:29 p.m.