Migrations


The toolbox supports importing from Progenesis QI, XCMS, HDF and Raw Bruker NMR data, and exporting to HDF.

The toolbox will import from these file formats into csm_spectra objects, supports exporting API objects to a standardised HDF format.

Raw Bruker Data - csm_import_raw_nmr

csm_import_raw_nmr is a new import system that imports, calibrates and interpolates spectra, and will import sample metadata and run basic analytical QC checks on the data.

Please see this guide for more information

Peak-picked MS data

Peak picked MS data can be imported using csm_import_spectra_xcms, csm_import_spectra_progenesis_qi.

HDF import and export

Spectra can be saved in HDF using csm_export_spectra_hdf and imported using csm_import_spectra_hdf.

To open HDF files on your PC for examining the contents you will need to install the HDFview from the HDF website

Sharing data and upgrading objects.

Matlab's object support has limitations, and sometimes you may experience issues updating code or sharing data with collaborators.

Unless the collaborator has the IMPaCTS toolboxes installed, they will not be able to import the data.

There are a few workarounds to this, including:

  1. Preferred - using the csm_object_converter utility to convert your objects into structs, and vice versa. These structs can be saved in .mat files.
  2. Extracting the intensity and chemical shift vectors of your spectra and saving those in .mat file.
  3. Using the HDF file format; csm_export_spectra_hdf will export csm_spectra objects to HDF.

Copyright Imperial College London 2019