bioio-imzml

A basic BioIO reader plugin for imzML mass spectrometry imaging (MSI) data, read with pyimzML.

Installation

pip install bioio-imzml

Requires a sibling .imzML + .ibd file pair (the standard imzML layout).

Usage

from bioio import BioImage

img = BioImage("sample.imzML")
img.dims.order  # "TCZYX" -- C is the m/z axis
img.channel_names  # m/z values, formatted as strings
img.data  # (T, C, Z, Y, X) numpy array

imzML-specific options (mz, mz_step, n_bins, mz_tolerance) work the same way through BioImage(..., mz=[...]), since BioImage forwards unrecognized keyword arguments straight to the reader. Or use the reader directly:

from bioio_imzml import Reader

# "processed" mode files (one m/z axis per pixel) need target channels:
reader = Reader("sample.imzML", mz=[798.54, 826.57, 885.55])

# reject a target with no real peak nearby instead of returning whatever
# peak happens to be closest, however far away. mz_tolerance is in the same
# units as mz itself (m/z, i.e. Da):
reader = Reader("sample.imzML", mz=[798.54, 826.57], mz_tolerance=0.005)

# or let the reader pick evenly spaced channels across the file's m/z range,
# either a fixed count (n_bins) or a fixed step (mz_step) in m/z units:
reader = Reader("sample.imzML", n_bins=512)
reader = Reader("sample.imzML", mz_step=0.1)

Continuous vs. processed mode

imzML stores spectra in one of two ways:

continuous: every pixel shares one m/z axis, so intensities already line up across pixels. Detected automatically (identical m/z byte offset and length for every spectrum) and read directly -- no resampling, no channel arguments needed.
processed: each pixel has its own m/z axis (typical for high-resolution profile data). There's no single true channel set, so this reader resamples every spectrum onto shared target m/z values by nearest-neighbor lookup, given via mz= or auto-generated with n_bins=.

reader.is_continuous reports which case applies to a given file.

Development

uv sync --extra test
uv run pytest
uv run ruff check .
uv run ruff format .
uv run ty check

Bump the version (updates pyproject.toml) and tag a release to publish to PyPI via CI:

uv version --bump patch  # or minor / major
git commit -am "Bump version"
git tag "v$(uv version --short)"
git push --tags

License

BSD-3-Clause

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