pyRadBio

Radiobiological modelling for ion-beam therapy, centred on the linear-quadratic (LQ) model

-ln S(D) = α D + β D²

pyRadBio computes ion- and energy-resolved α/β tables, z* tables, survival curves, RBE, and the dose required for a target survival level, for single ions and mixed radiation fields. It is built for research use (experiment planning, model comparison, table generation for treatment-planning research), MIT-licensed.

Model coverage

All models are implemented in pyRadBio and map a radiation field to the same LQ parameters (alpha, beta).

Family	Models	Package
LEM	LEM I, II, III, IV (+ GLOBLE)	pyradbio.models.lem
MKM	MKM, modified MKM, MCF MKM, SMK, OSMK 2021 / 2023, IMK	pyradbio.models.mkm
Phenomenological	13 LET-based proton RBE fits (Wilkens & Oelfke, Carabe, Frese, Wedenberg, McNamara, Mairani, ...)	pyradbio.models.phenomenological
RMF	Repair-Misrepair-Fixation with MCDS DSB yields	pyradbio.models.rmf
Katz	Cellular track-structure theory (ion kill + gamma kill)	pyradbio.models.katz
NanOx	Calibration and assembly layer; the ion route raises (its nanodosimetric Monte Carlo is not public)	pyradbio.models.nanox

MKMModel computes z* through a pluggable backend: pyRadBio's native engine (the default) or, as an independent cross-check, the external, MIT-licensed pyMKM (optional pyradbio[mkm] extra). Every model runs on pyRadBio's own track structure and microdosimetry.

By default LET comes from pyradbio.track.stopping_power.default_stopping_power: ICRU 90's procedure for Z 1-18 (within ~0.3% of ICRU 90 for p, alpha and C), Hubert, Bimbot & Gauvin's 1990 alpha scaling for Z 19-92 from 2.5 MeV/u, and an analytic Bethe formula anchored to them elsewhere (unvalidated there). The water tables in pyradbio.track.stopping (PSTAR/ASTAR/MSTAR, ICRU 49/73/90, Bethe with switchable corrections), Northcliffe & Schilling 1970, user SRIM tables, libdEdx, or pyMKM's tables are explicit opt-ins passed to a model's stopping_power; see docs/references/StoppingPower.md.

A shared, model-agnostic layer provides LQ survival/RBE, mixed-field dose-averaging, photon-reference and cell/target descriptions, and a benchmark harness against measured survival data. The full inventory, with every reference, is in ROADMAP.md.

Key references

• LEM I: Scholz & Kraft 1996, Adv. Space Res. 18, 5–14 — doi:10.1016/0273-1177(95)00784-C
• LEM II: Elsässer & Scholz 2007, Radiat. Res. 167, 319–329 — doi:10.1667/RR0467.1
• LEM III: Elsässer et al. 2008, Int. J. Radiat. Oncol. Biol. Phys. 71, 866–872 — doi:10.1016/j.ijrobp.2008.02.037
• LEM IV: Elsässer et al. 2010, Int. J. Radiat. Oncol. Biol. Phys. 78, 1177–1183 — doi:10.1016/j.ijrobp.2010.05.014; Friedrich et al. 2012, Int. J. Radiat. Biol. 88, 103–107 — doi:10.3109/09553002.2011.611213
• MKM (amorphous track): Kase et al. 2008, Phys. Med. Biol. 53, 37–59 — doi:10.1088/0031-9155/53/1/003
• modified MKM: Inaniwa et al. 2010, Phys. Med. Biol. 55, 6721 — doi:10.1088/0031-9155/55/22/008
• MCF MKM: Parisi et al. 2022 — doi:10.1088/1361-6560/ac7375
• SMK / OSMK: Inaniwa & Kanematsu 2018 — doi:10.1088/1361-6560/aabede; Inaniwa et al. 2021 — doi:10.1088/1361-6560/ac29cc; Inaniwa & Kanematsu 2023 — doi:10.1093/jrr/rrad049
• IMK: Matsuya et al. 2025, Med. Phys. — doi:10.1002/mp.70040
• Phenomenological RBE: Rørvik et al. 2018 — doi:10.1088/1361-6560/aad9db (review; each fit's own paper is cited in its module)
• RMF: Carlson et al. 2008, Radiat. Res. — doi:10.1667/RR1046.1
• Katz: Katz et al. 1971, Radiat. Res. — doi:10.2307/3573247
• NanOx: Cunha et al. 2017 — doi:10.1088/1361-6560/aa54c9; Monini et al. 2020 — doi:10.1667/RR15463.1
• pyMKM: Magro et al. 2025, Computation 13, 264 — doi:10.3390/computation13110264

Install

pyRadBio supports Python 3.10 to 3.14.

Using pyRadBio. The core install depends only on NumPy and SciPy. It covers every model, the LQ utilities, the stopping powers and the pyradbio command-line tool:

pip install pyradbio

Developing pyRadBio. Install an editable copy from a clone with the development tools and the extras the tests and scripts use. Add docs to build the documentation site (Python 3.11 or newer):

git clone https://github.com/e0404/pyRadBio.git
cd pyRadBio
pip install -e ".[all]"   # or ".[all,docs]"

The workflow and the checks to run before a pull request are in CONTRIBUTING.md.

Optional extras. Install only the extras you need. This command lists all of them:

pip install "pyradbio[tables,benchmark,fast,plot,dev,docs,mkm]"

• tables: pandas, pyarrow and openpyxl, for Parquet I/O, pandas views of the tables, Excel reading and the PIDE benchmark harness. CSV works without it.
• benchmark: python-dotenv, which reads the locations of external reference data from a local .env file.
• fast: numba, for the compiled LEM Monte-Carlo and radial-dose kernels.
• plot: matplotlib, for the examples/ and validation/ scripts. The library itself never imports it.
• dev: pytest, hypothesis, ruff, mypy and pre-commit, for running the tests and the linters.
• docs: Zensical and mkdocstrings, for building the documentation site. Needs Python 3.11 or newer.
• mkm: the external pyMKM package, which cross-checks the MKM family independently. It is never a default and is not part of all. It also keeps NumPy below 2.4.
• all: tables, benchmark, fast, plot and dev.

Quick start

Models live in pyradbio.models.* and are imported by name, so optional dependencies load only when you ask for them. The LQ utilities and the radiation, photon and cell descriptions are top-level.

from pyradbio import CellTarget, Ion, LQParameters, PhotonParameters
from pyradbio import dose_for_survival, rbe, survival
from pyradbio.models.lem.lem1 import LEM1

# V79 photon reference (Scholz & Kraft 1996; Elsässer & Scholz 2007)
photon = PhotonParameters(alpha_x=0.18, beta_x=0.028, D_t=30.0)
lem = LEM1(photon=photon, cell=CellTarget(nucleus_radius_um=5.0))

ab = lem.alpha_beta(Ion(Z=6, A=12, energy_MeV_u=11.0))  # LQParameters(alpha, beta)
s = survival(2.0, ab.alpha, ab.beta)  # surviving fraction at 2 Gy
d10 = dose_for_survival(0.10, ab.alpha, ab.beta)  # dose for 10% survival [Gy]
rbe10 = rbe(0.10, ab.alpha, ab.beta, reference=LQParameters(photon.alpha_x, photon.beta_x))

# MKM on the native z* backend (no extra needed); pyMKM is an opt-in cross-check
from pyradbio import Ion
from pyradbio.models.mkm import MKMModel

mkm = MKMModel()  # Inaniwa 2010 HSG defaults, native
ab = mkm.alpha_beta(Ion(Z=6, A=12, energy_MeV_u=100.0))

# from pyradbio.models.mkm.pymkm_backend import PyMKMBackend   # needs pyradbio[mkm]
# check = MKMModel(backend=PyMKMBackend())

# LET-based phenomenological RBE (here McNamara et al. 2015)
from pyradbio import PhotonParameters
from pyradbio.models.phenomenological import McNamara

mcn = McNamara(photon=PhotonParameters(alpha_x=0.18, beta_x=0.028))
ab = mcn.alpha_beta_from_let(5.0)  # dose-averaged LET [keV/um]
rbe10 = mcn.rbe_at_survival_from_let(5.0, 0.10)  # RBE at 10% survival

The examples/ folder has runnable demonstrations, one or more per model family; validation/ reconstructs published figures and compares against other codes and external data, reading the Monte-Carlo checkpoints that scripts/ generates.

Benchmark against measured survival data

pyradbio benchmark scores a model's initial-slope alpha (and RBE_alpha) against a database of measured LQ parameters. Three datasets are built in and the loader registry is user-extensible (pyradbio.benchmark.dataset):

• PIDE (default; tested against 3.4) is not bundled (registration-gated, non-redistributable). Obtain it from the GSI PIDE project page and drop the export into the git-ignored data/pide/ folder (or set PYRADBIO_PIDE_DIR).
• RadPhysBio (Zanni et al. 2024, CC BY 4.0) is open access: export the CSV from https://radbiodb.physics.ntua.gr/radphysbio/ into the folder named by PYRADBIO_RADPHYSBIO_DIR. Human cell lines only, and largely digitized; every report against it says so, together with how many ion rows could be paired with a same-publication photon reference. Its nominal beam energies restrict these benchmarks to LET-based models; energy-based routes are rejected.
• csv: your own file with columns cell, ion, energy, let, alpha_ion, beta_ion, alpha_x, beta_x (header-tolerant). energy may be left empty for LET-based models (a given energy is still filtered like any other); energy-based models require a supported target energy.

pyradbio benchmark --model lem4 --out benchmark_results/                    # PIDE from data/pide/
pyradbio benchmark --dataset radphysbio --model mcnamara --out rpb_results/
pyradbio benchmark --dataset csv --path mine.csv --model wedenberg --out mine_results/
pyradbio benchmark --pide /path/to/PIDE3.4.xlsx --model lem4 --out benchmark_results/   # explicit file

As an independent check, the LET-based models are validated against RadPhysBio with the second command above. RadPhysBio is by Zanni et al. 2024 (doi:10.3390/ijms25094729), licensed CC BY 4.0, and credited in THIRD_PARTY_NOTICES.md.

--model covers LEM I-IV, the MKM family (mkm, mmkm, smk, mcf, osmk2021, osmk2023, imk) at their published presets, RMF, four Katz parameter sets, and the thirteen phenomenological RBE fits (wilkens, carabe, frese, wedenberg, mcnamara, mairani, tilly2, tilly10, chen, jones, roru, peeler, unkelbach). Each report states what must be read alongside its numbers -- chief among them that this scores a model against measured data, not against a paper's own model line, and that the proton fits were themselves calibrated on much of the PIDE corpus.

Status

Research software under active development; the public API may still change. Each model is checked against its source papers by golden tests pinned to published values (pytest -m golden), and docs/references/ records every reconstruction, including where and why a result departs from the paper. See ROADMAP.md for planned and open work and AGENTS.md for the contributor/agent contract.

Citing

Every release is archived on Zenodo; doi:10.5281/zenodo.24046436 always resolves to the latest version, and the Zenodo page lists the DOI of each release. Cite the release you used (see CITATION.cff), together with the papers of the models you use.

License

MIT. See LICENSE. One exception: the Python port of MSTAR 3.12 (pyradbio/track/stopping/mstar/) is under its authors' freeware notice; see THIRD_PARTY_NOTICES.md.