Advanced Monte Carlo simulations of emission tomography imaging systems with GATE.

Built on top of the Geant4 toolkit, GATE is collaboratively developed for more than 15 years to design Monte Carlo simulations of nuclear-based imaging systems. It is, in particular, used by researchers and industrials to design, optimize, understand and create innovative emission tomography systems. In this paper, we reviewed the recent developments that have been proposed to simulate modern detectors and provide a comprehensive report on imaging systems that have been simulated and evaluated in GATE. Additionally, some methodological developments that are not specific for imaging but that can improve detector modeling and provide computation time gains, such as Variance Reduction Techniques and Artificial Intelligence integration, are described and discussed.

Scatter Correction Based on GPU-Accelerated Full Monte Carlo Simulation for Brain PET/MRI.

Accurate scatter correction is essential for qualitative and quantitative PET imaging. Until now, scatter correction based on Monte Carlo simulation (MCS) has been recognized as the most accurate method of scatter correction for PET. However, the major disadvantage of MCS is its long computational time, which makes it unfeasible for clinical usage. Meanwhile, single scatter simulation (SSS) is the most widely used method for scatter correction. Nevertheless, SSS has the disadvantage of limited robustness for dynamic measurements and for the measurement of large objects. In this work, a newly developed implementation of MCS using graphics processing unit (GPU) acceleration is employed, allowing full MCS-based scatter correction in clinical 3D brain PET imaging. Starting from the generation of annihilation photons to their detection in the simulated PET scanner, all relevant physical interactions and transport phenomena of the photons were simulated on GPUs. This resulted in an expected distribution of scattered events, which was subsequently used to correct the measured emission data. The accuracy of the approach was validated with simulations using GATE (Geant4 Application for Tomography Emission), and its performance was compared to SSS. The comparison of the computation time between a GPU and a single-threaded CPU showed an acceleration factor of 776 for a voxelized brain phantom study. The speedup of the MCS implemented on the GPU represents a major step toward the application of the more accurate MCS-based scatter correction for PET imaging in clinical routine.

Resolution modeling in projection space using a factorized multi-block detector response function for PET image reconstruction.

Positron emission tomography (PET) images usually suffer from limited resolution and statistical uncertainties. However, a technique known as resolution modeling (RM) can be used to improve image quality by accurately modeling the system's detection process within the iterative reconstruction. In this study, we present an accurate RM method in projection space based on a simulated multi-block detector response function (DRF) and evaluate it on the Siemens hybrid MR-BrainPET system. The DRF is obtained using GATE simulations that consider nearly all the possible annihilation photons from the field-of-view (FOV). Intrinsically, the multi-block DRF allows the block crosstalk to be modeled. The RM blurring kernel is further generated by factorizing the blurring matrix of one line-of-response (LOR) into two independent detector responses, which can then be addressed with the DRF. Such a kernel is shift-variant in 4D projection space without any distance or angle compression, and is integrated into the image reconstruction for the BrainPET insert with single instruction multiple data (SIMD) and multi-thread support. Evaluation of simulations and measured data demonstrate that the reconstruction with RM yields significantly improved resolutions and reduced mean squared error (MSE) values at different locations of the FOV, compared with reconstruction without RM. Furthermore, the shift-variant RM kernel models the varying blurring intensity for different LORs due to the depth-of-interaction (DOI) dependencies, thus avoiding severe edge artifacts in the images. Additionally, compared to RM in single-block mode, the multi-block mode shows significantly improved resolution and edge recovery at locations beyond 10 cm from the center of BrainPET insert in the transverse plane. However, the differences have been observed to be low for patient data between single-block and multi-block mode RM, due to the brain size and location as well as the geometry of the BrainPET insert. In conclusion, the RM method proposed in this study can yield better reconstructed images in terms of resolution and MSE value, compared to conventional reconstruction without RM.

Boot swabs to collect environmental samples from common locations in dairy herds for Mycobacterium avium ssp. paratuberculosis (MAP) detection.

The aim of the present study was the examination of the boot swab sampling technique for the collection of environmental material in order to identify Mycobacterium avium ssp. paratuberculosis (MAP)-infected herds. Eight dairy herds were included into the study. Four of them had a well-known history of MAP-infection from a herd surveillance programme conducted since 2006. Cows in these herds were repeatedly tested positive in Pourquier® MAP-ELISA (Pourquier, Montepellier, France); in some MAP could be isolated in individual faecal culture despite that symptoms of paratuberculosis were never reported. In four presumably negative herds nearly all cows were repeatedly tested serologically negative for MAP. The pathogen was never isolated from faecal samples of cows by culture. The study was initiated with the aim of standardising environmental samples as a herd diagnostics, in which overall 130 pairs of boot swab samples from the cows' surroundings were taken In 58 of 64 swab samples (90·6%) from confirmed MAP-infected herds the organism could be isolated by mycobacterial culture of the boot swab. Contrarily, in 66 samples from presumably MAP-negative herds only one swab was positive (1·5%). The utilisation of boot swabs as a standardised technique for environmental sampling offers an effective and inexpensive tool for identifying herds infected with MAP. This is the first report of using boot swabs for the collection of environmental samples for MAP- detection in cattle herds. This easy to perform technique enables the economical detection of MAP herd status.

[Evaluation of the diagnosis of subclinical endometritis in dairy cattle using ultrasound]. / Evaluierung der Diagnostik subklinischer Endometritiden mittels Ultraschall beim Rind.

The aim of this study was to determine signs of subclinical endometritis found by ultrasound that are associated with reduced fertility in dairy cows. The maximum diameter of the uterine lumen was determined by ultrasound in 324 cows without clinical signs of endometritis after evaluation of the genital tract 21 to 27 days postpartum. Cows were classified into healthy or with subclinical endometritis by three threshold values for the maximum uterine lumen diameter of 0.2 cm, 0.5 cm or 0.8 cm. Examinations by rectal palpation and ultrasound as well as classifications were repeated 14 days later. In addition, ovaries were scanned by ultrasound to determine the stage of the estrous cycle. In a subgroup of 103 cows the echotexture of the uterus and its contents was evaluated. In these cows the diagnosis of subclinical endometritis was performed by a scoring system. The diameter of the uterine lumen was significantly affected by stage of the estrous cycle at the time of examination. However, no effects were found for the stage of the cycle at the time of examination on subsequent reproductive performance. A uterine lumen with a maximum diameter of more than 0.2 cm showed a significant negative association with conception rate and proportion of cows pregnant. Classification based on higher threshold values did not reveal an association with reproductive performance. Echogenic content in the uterus also decreased reproductive performance. A classification based on the echotexture of the uterus and its contents revealed significant differences between healthy cows and cows with subclinical endometritis regarding the proportion of cows inseminated and pregnant. The results of this study showed that the diagnostic of bovine endometritis should be broadend by ultrasonography. The definition of subclinical endometritis diagnosed by means of ultrasonography has to be evaluated in further studies.