Glossary¶

Words you will meet in these pages, in plain language. The computer terms come first, then the mass spectrometry ones.

Computer terms¶

Terminal: A window where you type commands. On Windows it is called PowerShell; on macOS and Linux, Terminal.
Command: A line you type into the terminal and run with Enter, such as thyra --version.
Path: The address of a file or folder, such as /Volumes/data/MSI/brain.d on macOS. On Windows, a path starts with a drive letter, such as D:.
Python: The programming language Thyra is written in. You need it installed, but you do not need to write any.
pip: Python's standard installer for packages such as Thyra.
uv: A fast installer for Python programs. It can also fetch the right version of Python for you.
Environment: A separate set of Python packages, so that the packages of one project do not interfere with another's. Tools such as conda and uv create them.
Jupyter notebook: A document that mixes text with Python code you can run piece by piece. The Explore the result in Python page is one.
SpatialData: An open format and Python library for spatial data from biology, such as imaging mass spectrometry. Thyra saves your data in this format.
Zarr: The way SpatialData stores data on disk: a folder of many small files that programs can read a piece at a time. That is why the result is a folder ending in .zarr.
Table (AnnData): The part of the result that holds the spectra: one row per pixel, one column per m/z bin. AnnData is the name of the Python format for such tables.
scverse: A community of open-source Python tools for single-cell and spatial biology. SpatialData, napari-spatialdata, scanpy and squidpy belong to it.
napari: A free image viewer. With the napari-spatialdata plugin, it opens SpatialData results.
Command-line option: An extra instruction added to a command, starting with --, such as --pixel-size 50.

Mass spectrometry terms¶

MSI (mass spectrometry imaging): Recording a mass spectrum at every point of a sample, so that each m/z value can be shown as an image.
m/z: Mass-to-charge ratio, the x-axis of a mass spectrum.
Spectrum: The intensities measured at one pixel, across the m/z range.
Pixel size: The distance between neighbouring measurement points, in micrometres.
TIC (total ion current): The sum of all intensities in one spectrum. A TIC image shows it for every pixel, and gives a quick overview of the sample.
Ion image: An image of the intensity of one m/z value, or a narrow range around it, across all pixels.
Profile and centroid data: Profile data records the full shape of each peak. Centroid data keeps one point per peak.
Resampling and m/z bins: Instruments record each spectrum at slightly different m/z values. Resampling moves every spectrum onto one shared set of m/z positions, called bins, so that the same column means the same m/z in every pixel.
Region: A separately defined area of an acquisition, for example one tissue section on a slide that holds several.
Optical image: A photo or microscope scan of the slide, taken before the measurement.
Teaching points: Marks that link positions in the optical image to positions of the instrument's stage. Thyra uses them to lay the MSI data over the photo.
imzML: An open file format for imaging mass spectrometry. It comes as two files: an .imzML file that describes the data and an .ibd file that holds the numbers.
Ion mobility (TIMS): A separation of ions by their size and shape, in addition to m/z. Bruker timsTOF instruments measure it with trapped ion mobility spectrometry (TIMS).
1/K0: The unit of ion mobility on a timsTOF: the inverse reduced mobility, in V s/cm2. Larger ions of the same charge have a larger 1/K0.
Mass-mobility heatmap: A picture of the whole image in two dimensions: m/z against mobility. Two spots at one m/z but at different mobility are two different ions.
CCS (collision cross section): A size measure of an ion, worked out from its mobility. The mobility table holds it in the column ccs, in square angstroms. Thyra assumes each ion has charge 1.
MS/MS: Tandem mass spectrometry: selected ions are broken into fragments, and the fragments are measured.
Precursor and fragment: In MS/MS, the precursor is the ion the instrument selects. The fragments are the pieces it breaks into.
PASEF and iprm-PASEF: Bruker timsTOF methods that select precursors one after the other as they leave the mobility separation. In imaging, iprm-PASEF fragments the same list of precursors at every pixel.