SEED — Spectral Extraction & Encoding Driver

A cross-platform mass spectrometry file reader used by LEAF. It runs without .NET on supported platforms.

SEED reads mass spectrometry files from 7 vendor formats directly from their binary formats. It provides a CLI tool, a desktop GUI converter, and Python bindings with NumPy integration.

Supported vendors: Thermo, Bruker, Waters, Agilent, Shimadzu, Sciex, plus the open mzML standard.

Public release status

Public binaries and the pip install seed wheel are currently unavailable while SEED prepares its 0.x public relaunch. Build from source until then — see Install below.

Supported formats

Format	Extension	Read	Convert to mzML	Notes
Thermo RAW	.raw	Full	Yes	Versions 57-66; all Orbitrap / LTQ / Astral instruments
Bruker TDF / TSF	.d	Full	Yes	timsTOF (4D ion mobility), QTOF
Waters .raw	.raw (directory)	Full	Yes	MassLynx SQD2, ZQ, SIR / MRM
Agilent .d	.d (directory)	Full	Yes	MassHunter + ChemStation
Shimadzu LCD	.lcd	Full	Yes	MRM, triple-quad
Sciex WIFF	.wiff	Metadata	Planned	OLE2 metadata extraction
mzML	.mzml, .mzml.gz	Full	N/A	Indexed + non-indexed, gzip

Vendor format details

• Thermo RAW — versions 57-66, centroid / profile / FT / LT decoders, trailer metadata (86+ fields). No .NET required.
• Bruker .d — SQLite + zstd-compressed binary blobs, TOF-to-m/z quadratic calibration, full ion mobility (1/K0), ddaPASEF and diaPASEF support.
• Waters .raw — all 4 MassLynx binary encodings (2 / 4 / 6 / 8-byte), polynomial m/z calibration, multi-function support.
• Agilent .d — MassHunter (MSScan.bin + MSPeak.bin / MSProfile.bin) and ChemStation (DATA.MS big-endian) sub-formats.
• Sciex WIFF — OLE2 metadata extraction; scan data decoding pending (format is not publicly documented).

Install

CLI

Build from source while the public binary release pipeline is dormant:

git clone https://github.com/EstrellaXD/seed-core
cd seed-core
cargo build --release -p seed-cli
# → target/release/seed

Place the binary on PATH. The binary is static, ~2 MB, and has no runtime dependencies.

Python

git clone https://github.com/EstrellaXD/seed-core
cd seed-core/crates/seed-py
maturin develop --release

Requires Python 3.11+, maturin, and a Rust toolchain.

GUI converter

Build from crates/seed-gui (Tauri v2 + Vue 3):

cd seed-core/crates/seed-gui
bun install
bun tauri build

The GUI provides drag-and-drop RAW-to-mzML conversion with progress bars. Build artifacts land in src-tauri/target/release/bundle/.

Where to next

• → Command line — seed subcommand reference
• → Changelog — release history

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LEAF, the metabolomics analysis platform built on top of SEED, has its own user manual: LEAF Get Started.