Selected papers

A few papers, each with a short explanation, a schematic and a figure from the paper. The full list is on the publications page.

GATE 10

Journal
GATE 10 Monte Carlo Particle Transport Simulation: I. Development and New Features
Sarrut D., Arbor N., Baudier T., Bert J., Chatzipapas K., Favaretto M., … (33 authors) · Physics in Medicine & Biology, 71(1), 015042, 2026
Journal
GATE 10 Monte Carlo Particle Transport Simulation: II. Architecture and Innovations
Krah N., Arbor N., Baudier T., Bert J., Chatzipapas K., Favaretto M., …, Sarrut D. (33 authors) · Physics in Medicine & Biology, 71(1), 015043, 2026

GATE 10 is a complete re-implementation of GATE, the open-source Monte Carlo platform for medical physics built on Geant4. Simulations are now plain Python scripts, run multithreaded, and GATE can be embedded as a library in other software. Part I presents the new features, Part II the architecture behind them.

Your Python scriptimport opengate as gatesim = gate.Simulation()sim.add_source(...)sim.add_actor(...)sim.run()opengatePython user interfaceopengate_libC++ runtime (speed)Geant4via pybind11 bindingsmultithreadingusable as a librarytime-aware sourcesLET, RBE scoringopen developmentPart I: new features · Part II: the architecture behind them
Prostate brachytherapy dose (isodoses) simulated with the new "parallel worlds" feature.
Prostate brachytherapy dose (isodoses) simulated with the new "parallel worlds" feature. Figure: Sarrut et al. 2026, Phys. Med. Biol., CC BY 4.0.

FFAA

Journal
Free flight angular acceptance (FFAA) variance reduction technique for SPECT Monte Carlo simulations
Sarrut D., Etxebeste A., Jacquet M., Létang J. M. · Physics in Medicine and Biology, 71(9), 095009, 2026

A variance reduction technique that makes SPECT Monte Carlo simulations about 100 to 200 times faster, without pre-computed detector response or training: primary photons are forced towards the detector, scattered photons are split and kept only when they can reach it, and the collimator and detector stay fully simulated.

×100–200 fasterpatient (CT)sourceSPECT headfull analogMonte Carloprimary: forced direction+ free flight (weighted)scatter: split, kept only insidethe acceptance cone
Reconstructed images from the reference analog simulation (top) and FFAA (bottom).
Reconstructed images from the reference analog simulation (top) and FFAA (bottom). Figure: Sarrut et al. 2026, Phys. Med. Biol., CC BY 4.0.

Jacobian-Free Unrolling

Journal
Jacobian-Free Unrolling: memory efficient unrolled network for 3D SPECT Reconstruction
Constanza C., Kaprelian T., Etxebeste A., Sarrut D. · IEEE Transactions on Radiation and Plasma Medical Sciences, 2026

Deep "unrolled" reconstruction networks are hard to train for fully 3D SPECT because they need too much GPU memory. Jacobian-Free Unrolling back-propagates through the last iteration only, which makes 3D training possible, with better images than OSEM and MAPEM on simulated, phantom and patient ¹⁷⁷Lu data.

x₀MAPEM step+ CNN priorMAPEM step+ CNN prior⋯MAPEM step+ CNN priorx̂lossgradient through the last iteration onlyearlier iterations: no computational graph stored→ fully 3D training fits in GPU memory
Reconstructions of simulated data with the different methods (JFU-MAPEM in the bottom right).
Reconstructions of simulated data with the different methods (JFU-MAPEM in the bottom right). Figure: Constanza et al. 2026, IEEE TRPMS, accepted manuscript (© IEEE).

Partial volume correction with deep learning

Journal
Partial Volume Correction of SPECT Images With Deep Learning Trained on Synthetic Data
Kaprélian T., Etxebeste A., Sarrut D. · IEEE Transactions on Radiation and Plasma Medical Sciences, 1–1, 2025

Partial volume effects blur small structures in SPECT and bias activity estimates, a key issue for ¹⁷⁷Lu dosimetry. Neural networks trained only on synthetic data correct them in the projections, in the image, or in both (hybrid); the hybrid version gave the best noise/resolution trade-off, with errors reduced by a third on a simulated patient.

synthetic trainingrandom organs, lesions,activity distributionsSPECTprojectionsrecon.SPECT imageblurred (PVE)corrected imagesharper, quantitativeCNN sinoCNN imghybrid: both domainshybrid, simulated patient:NRMSE −33 %noise −80 %
The five correction methods compared with the ground truth on simulated data.
The five correction methods compared with the ground truth on simulated data. Figure: Kaprélian et al. 2025, IEEE TRPMS, CC BY 4.0.

Predicting PSA50 response

Journal
Predicting PSA50 Response to 177Lu-PSMA Therapy Using Machine Learning and Automated Total Tumor Volume
Rios-Sanchez E., Giraudet A.-L., Sanchez-Lajusticia A., Pretet V., Paquet E., Baudier T., Badel J.-N., Sarrut D. · EJNMMI Physics, 12(1), 95, 2025

Can a PET/CT made before treatment predict which patients will respond to ¹⁷⁷Lu-PSMA therapy? The total tumour volume is extracted automatically from ⁶⁸Ga-PSMA PET/CT, and machine-learning models predict the PSA50 response of 139 patients as well as existing nomograms.

before treatment⁶⁸Ga-PSMAPET/CTautomatictumour volumeimage andclinical dataML modelLASSO, SVMPSA50responder?139 patients treated with ¹⁷⁷Lu-PSMA (real-world data)F1 ≈ 0.68, comparable to existing nomograms
Automatic extraction of the total tumour volume from ⁶⁸Ga-PSMA PET/CT.
Automatic extraction of the total tumour volume from ⁶⁸Ga-PSMA PET/CT. Figure: Rios-Sanchez et al. 2025, EJNMMI Physics, CC BY 4.0.

Reducing the imaging workload of ¹⁷⁷Lu dosimetry

Journal
A review of 177Lu dosimetry workflows: how to reduce the imaging workloads?
Vergnaud L., Dewaraja Y. K., Giraudet A.-L., Badel J.-N., Sarrut D. · EJNMMI Physics, 11(1), 65, 2024

Dosimetry can personalise ¹⁷⁷Lu therapy, but it needs several SPECT/CT scans after injection. This review describes how to reduce that burden, with fewer or shorter acquisitions down to a single time point, with their assumptions and limits, for ¹⁷⁷Lu-DOTATATE and ¹⁷⁷Lu-PSMA.

0123456days after injectionstandard4–5 SPECT/CTreduced2 time pointssingle time point+ model assumptionsless imaging workload, more assumptions
Table 2 of the review: hypotheses, methods and effective half-lives used for dosimetry based on a single acquisition.
Table 2 of the review: hypotheses, methods and effective half-lives used for dosimetry based on a single acquisition. Figure: Vergnaud et al. 2024, EJNMMI Physics, CC BY 4.0.

Photon source model for alpha emitters

Journal
A Photon Source Model for Alpha-Emitter Radionuclides
Sarrut D., Etxebeste A., Létang J. M. · Physics in Medicine & Biology, 69(9), 095009, 2024

PHID emits directly the photons of the whole decay chain of alpha-emitter radionuclides such as ²²⁵Ac, with the right energies and timing (Bateman equations), instead of simulating every decay. About 30 times faster in a typical example, for any alpha emitter in Geant4, and open source in GATE 10.

≈ 30× fasterdecay chain of ²²⁵Ac²²⁵Ac²²¹Fr²¹⁷At²¹³Bi⋮PHID source modelphoton lines from Geant4 data:isomeric transitions+ atomic relaxationtiming: Bateman equationsphotons only,right energiesand timeno need to simulate every decay of the chainany alpha emitter in Geant4 · open source in GATE 10
²²⁵Ac SPECT projections of the IEC phantom with the reference ion source, a simplified two-line source and PHID, and their profiles.
²²⁵Ac SPECT projections of the IEC phantom with the reference ion source, a simplified two-line source and PHID, and their profiles. Figure: Sarrut et al. 2024, Phys. Med. Biol., CC BY 4.0.

GAN for SPECT Monte Carlo simulation

Journal
Modeling Complex Particles Phase Space with GAN for Monte Carlo SPECT Simulations: A Proof of Concept
Sarrut D., Etxebeste A., Krah N., Létang J.-M. · Physics in Medicine and Biology, 2021

A generative adversarial network (GAN) learns the particles exiting the patient. Combined with a neural network for the detector response, it simulates a full rotating SPECT acquisition without tracking the particles in the patient, with reduced computation time (proof of concept).

referencepatient CT+ activitytrack every particlein the patient (slow)detectorMonte Carloproposedpatient CT+ activityGAN generatorparticles exiting the patientARF networkdetector responsefull rotating SPECT acquisition, reduced computation time
SPECT reconstructed from the reference Monte Carlo simulation (top) and from the GAN-based simulation (bottom).
SPECT reconstructed from the reference Monte Carlo simulation (top) and from the GAN-based simulation (bottom). Figure: Sarrut et al. 2021, Phys. Med. Biol., accepted manuscript (© IOP Publishing).

GAN for compact beam source models

Journal
Generative Adversarial Networks (GAN) for Compact Beam Source Modelling in Monte Carlo Simulations
Sarrut D., Krah N., Letang J.-M. · Physics in Medicine and Biology, 64(21), 2019

A phase-space file of several gigabytes is replaced by a compact GAN of about 10 MB that generates particles on demand. Dose distributions for linac beams and brachytherapy seeds agree with the reference within 1 % voxel by voxel.

phase-space filelinac beam orbrachytherapy seeda few GBtrainGAN generator0.5 M weights≈ 10 MBsampleparticles on demand→ Monte Carlo dosedose within 1 % of the reference, voxel by voxel(sharp energy lines not perfectly reproduced)
Prostate brachytherapy dose from the phase-space file (left), from the GAN (centre), and their difference.
Prostate brachytherapy dose from the phase-space file (left), from the GAN (centre), and their difference. Figure: Sarrut et al. 2019, Phys. Med. Biol., accepted manuscript (© IOP Publishing).

Voxel-based multi-model fitting (VoMM)

Journal
Voxel-based multi-model fitting method for modelling time activity curves in SPECT images
Sarrut D., Halty A., Badel J., Ferrer L., Bardiès M. · Medical Physics, 44, 6280-6288, 2017

Voxel-based dosimetry needs a fit of the time-activity curve of every voxel. Instead of the same model for all voxels, VoMM selects for each voxel the most appropriate model among several (Akaike criterion): errors on the time-integrated activity below 5 % instead of over 10 % in simulations, and 90 % of the voxels fitted on patient data.

SPECT over timeone voxelits time-activity curvetimebest model per voxelAkaike criterion→ time-integrated activityTIA error < 5 % (vs > 10 % with a single model, simulations)90 % of patient voxels fitted
Time-integrated activity with a single model (left) and VoMM (right); yellow voxels could not be fitted.
Time-integrated activity with a single model (left) and VoMM (right); yellow voxels could not be fitted. Figure: Sarrut et al. 2017, Medical Physics (© AAPM).

Lymph node stations from relative positions

Journal
Learning directional relative positions between mediastinal lymph node stations and organs
Sarrut D., Rit S., Claude L., Pinho R., Pitson G., Bouilhol G., Lynch R. · Medical Physics, 41(6), 061905, 2014

Mediastinal lymph node stations are defined by their position relative to the organs around them. These directional relations are learned automatically from expert delineations, then used to segment the stations on new CT images (mean Dice 66 %). The database of the five reference cases is publicly available.

axial CT slice (schematic)tracheaaortaspine?learned relations (examples)“below and right of the trachea”“left of the aorta”“in front of the spine”… about 30 per stationfuzzy maps → station segmentationmean Dice 66 %, distance 1.7 mm5 reference cases, open database
Lymph node stations delineated by experts on thoracic CT slices.
Lymph node stations delineated by experts on thoracic CT slices. Figure: Sarrut et al. 2014, Medical Physics (© AAPM).

Spatio-temporal motion estimation in 4D CT

Journal
Spatio-Temporal Motion Estimation for Respiratory-Correlated Imaging of the Lungs
Vandemeulebroucke J., Rit S., Kybic J., Clarysse P., Sarrut D. · Medical Physics, 38(1), 2011

Estimating lung motion in 4D CT is difficult because of artefacts. Instead of registering each breathing phase separately, the motion of every point over the whole respiratory cycle is modelled as one smooth cyclic trajectory (B-splines in space and time), which is more robust to artefacts.

frame by frameeach breathing phase registered alonean artefact (phase 4) breaks the trajectoryspatio-temporalone cyclic B-spline trajectoryfor the whole cycleinhaleone respiratory cycle
Motion fields with a simulated artefact (bottom row): (a) phase-by-phase registration, (b) spatio-temporal model.
Motion fields with a simulated artefact (bottom row): (a) phase-by-phase registration, (b) spatio-temporal model. Figure: Vandemeulebroucke et al. 2011, Medical Physics (© AAPM).