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Which files can I convert?

Thyra reads the files your instrument writes. Point it at the file or folder in the table, and it recognises the format by itself.

Your instrument Point Thyra at Windows Linux macOS
Any instrument that exports imzML the .imzML file yes yes yes
Bruker timsTOF the folder ending in .d yes yes no
Bruker solariX the folder ending in .d yes yes yes
Bruker rapifleX the acquisition folder yes yes yes
Waters (MassLynx) the folder ending in .raw yes yes no
PHI nanoTOF (ToF-SIMS) the file ending in .raw yes yes yes
mzPeak (experimental) the .mzpeak file yes yes yes

Your instrument is not listed? Most instrument software can export imzML, and Thyra converts that. For Shimadzu data, export imzML from IMAGEREVEAL MS; native support for Shimadzu files is in development.

Check a dataset before you convert it

To see what Thyra finds in a dataset without converting it, run:

thyra metadata my_slide.d

It prints what Thyra can tell about the acquisition: the instrument, the polarity, the pixel size and more. If no pixel size appears, the conversion will need --pixel-size.

Advanced: What thyra metadata prints

The output is a JSON document in the same form Thyra stores inside every result. Add -o description.json to save it to a file instead. For Waters data, Thyra reads every spectrum to describe the run, so it can take a while. Describe and share your data explains the document.

imzML

  • Keep the .ibd file next to the .imzML file, with the same name. Thyra needs both.
  • Thyra reads the pixel size from the file when the file records it. If it does not, give it with --pixel-size.
  • A file with several z-slices becomes one dataset per slice. Add --handle-3d to keep them together as one 3D volume.
  • A file with a mobility array is read too. See Ion mobility and MS/MS.
  • If Thyra refuses the file, see Troubleshooting.

Bruker timsTOF

  • Point Thyra at the .d folder. You can also point it at the folder above: if that holds several .d folders, Thyra asks which one to convert.
  • Keep the .mis file from flexImaging next to the .d folder, ideally with the same name. It gives the pixel size and lines the data up with the optical image.
  • Thyra adds every image it finds (TIFF, JPEG, PNG or BMP). It looks in the .d folder, in the folder you pointed at, and in the folder above the .d. Unrelated pictures in those folders end up in the result too. To leave all images out, add --no-optical.
  • A slide with several regions is converted as one dataset, with every pixel labelled with its region. To convert only one region, see Change how Thyra converts.
  • Ion mobility (TIMS) and PASEF MS/MS data are kept automatically. See Ion mobility and MS/MS.
  • Close Bruker DataAnalysis before converting. While it has the dataset open, Thyra cannot read it.
Advanced: ion mobility and MS/MS options

For TIMS data, Thyra sums each spectrum over the mobility dimension and also stores a mass-mobility heatmap. It can add a table that keeps mobility per pixel (--mobility-grid). PASEF MS/MS acquisitions get a separate table with the fragments split by precursor. The command-line options page describes these options.

Bruker solariX

  • Point Thyra at the .d folder itself. It must hold the files peaks.sqlite and ImagingInfo.xml.
  • The pixel size comes from a .mis file next to the .d folder. Without one, give it with --pixel-size.
  • A .d folder that holds only raw transients, with no peaks.sqlite, cannot be read. Export imzML from DataAnalysis, SCiLS Lab or flexImaging, and convert that instead.
  • Optical images are added, but they are not lined up with the MSI data.

Bruker rapifleX

  • Point Thyra at the acquisition folder, not at the .d folder inside it. The folder must hold the .dat, _poslog.txt and _info.txt files.
  • The pixel size comes from the _info.txt file.
  • A .mis file in the folder lines the data up with the optical image.

Waters (MassLynx)

  • Point Thyra at the .raw folder, and copy the folder whole: if any _FUNC file is missing, Thyra stops.
  • The pixel size comes from the recorded laser positions.
  • Synapt runs with ion mobility on keep their drift times. Older Synapt G1 runs with ion mobility on are refused: the Waters library cannot read them safely.
  • When a run records low and high collision energy over the same pixels (MSe), Thyra keeps the low-energy data.
Advanced: profile and centroid data from Waters

Waters runs can be read as profile spectra or as centroids. For SELECT SERIES MRT data, Thyra reads the profile by default, which gives a larger result. The command-line options page shows how to choose.

PHI nanoTOF (ToF-SIMS)

  • Point Thyra at the .raw file. Unlike Waters data, it is a single file.
  • The pixel size comes from the file.
  • A mosaic of tiles is joined into one image, and the frames of a depth profile are added into one 2D image.
  • Mosaic, MS/MS and depth-profile acquisitions have so far been tested only on synthetic files. If you have real data of these kinds, please get in touch.

mzPeak (experimental)

  • Point Thyra at the .mzpeak file. Only 2D images are read.
  • Thyra reads the pixel size only when the file records it.

Go deeper

Supported formats explains how each format is recognised and read, in full detail.