M. V. Martins

A plant’s perspective of extremes: Terrestrial plant responses to changing climatic variability

We review observational, experimental, and model results on how plants respond to extreme climatic conditions induced by changing climatic variability. Distinguishing between impacts of changing mean climatic conditions and changing climatic variability on terrestrial ecosystems is generally underrated in current studies. The goals of our review are thus (1) to identify plant processes that are vulnerable to changes in the variability of climatic variables rather than to changes in their mean, and (2) to depict/evaluate available study designs to quantify responses of plants to changing climatic variability. We find that phenology is largely affected by changing mean climate but also that impacts of climatic variability are much less studied, although potentially damaging. We note that plant water relations seem to be very vulnerable to extremes driven by changes in temperature and precipitation and that heat-waves and flooding have stronger impacts on physiological processes than changing mean climate. Moreover, interacting phenological and physiological processes are likely to further complicate plant responses to changing climatic variability. Phenological and physiological processes and their interactions culminate in even more sophisticated responses to changing mean climate and climatic variability at the species and community level. Generally, observational studies are well suited to study plant responses to changing mean climate, but less suitable to gain a mechanistic understanding of plant responses to climatic variability. Experiments seem best suited to simulate extreme events. In models, temporal resolution and model structure are crucial to capture plant responses to changing climatic variability. We highlight that a combination of experimental, observational, and/or modeling studies have the potential to overcome important caveats of the respective individual approaches.

List-mode maximum-likelihood reconstruction for the ClearPEM system

A dedicated implementation of list-mode maximum-likelihood expectation-maximization (MLEM) reconstruction for the ClearPEM system is presented. The system is composed of two face-to-face detectors, which can be rotated to acquire data from different angular positions. Due to the specific design with irregular sampling and depth of interaction capability, the possible number of lines of response (LOR) is significantly greater than the number of detected events in a standard clinical study. Because reconstruction methods based on data histogramming to sinogram lead to a high computational cost and/or a loss of the intrinsical system resolution, it is necessary to consider the processing of events in list-mode during the reconstruction. The presented method adopted EM algorithm to maximize the logarithmic likelihood function that is expressed in list-mode. The voxel efficiency is corrected by pre-calculated efficiency maps based on flood phantom acquisitions. The method is also implemented with parallelization by distributing the calculation of the acquired events into different threads for significantly increasing computational speed. The results of a Derenzo phantom study show that the presented algorithm can achieve a similar result as 3D-OSEM reconstruction based on data histogramming with significantly lower reconstruction time (6 times faster with one thread, 20 times faster with 8 threads distributed in 8 CPU cores). In clinical studies with lower acquired events, the acceleration ratio can be even higher. The result from a breast phantom study shows that lesions with 15 mm in diameter, each, as well as a small lesion with 5 mm in diameter are clearly visible and can be characterized. The mouse imaging studies show also great potential of the system in small animal applications.

Clear-PEM: Monte Carlo performance and image reconstruction studies

The Clear-PEM prototype under development aims to improve early stage breast cancer diagnostics. The proposed device is based on cerium doped lutetium crystal matrices developed by the Crystal Clear Collaboration, as well as on modern data acquisition techniques. A series of Monte Carlo studies were performed to evaluate detection sensitivity, background rate and intrinsic spatial resolution in order to optimize the final detector concept. A description of the developed GEANT4 based simulation framework and PEM image reconstruction software is also presented in this paper. First simulation results indicates that Clear-PEM design significantly increases detection sensitivity in comparison with conventional PET cameras for breast cancer diagnostics. Count-rate simulation results are within operation limits for the data acquisition system, able to read 1 MHz event rate, allowing to take full profit of the large detector acceptance.

An overview of the Clear-PEM breast imaging scanner

We present an overview of the Clear-PEM breast imaging scanner. Clear-PEM is a unique dual-head Positron Emission Mammography scanner using APD-based detector modules that are capable of measuring depth-of-interaction (DOI) with a resolution of 2 mm in 20 mm long LYSO:Ce crystals. Such capability leads to an image spatial resolution of 1.2 mm and a high efficiency, foreseeing the detection of 3 mm breast lesions in less than 7 minutes exams. The full system comprises 192 detector modules in a total of 6144 LYSO:Ce crystals and 384 32-pixel APD arrays readout by ASICs with 192 input channels that represents an unprecedented level of integration in PET systems. Throughout the project and besides the detector module, we had developed dedicated Frontend and Data Acquisition electronics, the mechanical design and construction of the detector heads and the robotic gantry, as well as all the software that include calibration (energy, time and DOI), normalization and image reconstruction algorithms. In this work we will discuss the developments and present the commissioning results of the detector before the beginning of the clinical trials program, scheduled for the end of the present year.

System matrix calculation for Clear-PEM using ART and linograms

The Clear-PEM device is a positron emission mammography (PEM) unit based on planar detectors and is currently under development. We have developed a 2D algebraic reconstruction technique (ART) algorithm using linograms to reconstruct Clear-PEM data. In this work we evaluate three different methods of calculating the system matrix used by the ART algorithm, which we designate as the pixel-, ray- and tube-driven methods, respectively. The methods were tested using Monte Carlo simulated data. The results obtained show that ART algorithm allows, for these cases, accurate image reconstruction and indicate that a more accurate modeling of the image system matrix using tubes of response (TORs) provides the best image evaluation indexes.

Characterization of the Clear-PEM breast imaging scanner performance

We present results on the characterization of the Clear-PEM breast imaging scanner. Clear-PEM is a dual-head Positron Emission Mammography scanner using APD-based detector modules that are capable of measuring depth-of-interaction (DOI) with a resolution of 2 mm in LYSO:Ce crystals. The full system comprises 192 detector modules in a total of 6144 LYSO:Ce crystals and 384 32-pixel APD arrays readout by ASICs with 192 input channels, which represents an unprecedented level of integration in APD-based PET systems. The system includes Frontend and Data Acquisition electronics and a robotic gantry for detector placement and rotation. The software implements calibration (energy, time and DOI), normalization and image reconstruction algorithms. In this work, the scanner main technical characteristics, calibration strategies and the spectrometric performance in a clinical environment are presented. Images obtained with point sources and extended uniform sources are also presented. The first commissioning results show 99.7% active channels. After calibration, the dispersion of the channels absolute gain is 15.3%, which demonstrate that despite the large number of channels the system is rather uniform. The mean energy resolution at 511 keV is 15.9% for all channels, and the mean DOI constant is 5.9%/mm, which is consistent with a 2 mm DOI resolution, or better. The coincidence time resolution at 511 keV, for a energy window between 400 and 600 keV, is 5.2 ns FWHM. The image resolution measured with point sources was found to be of the order of 1.3 mm FWHM. The DOI capability was found to have a strong impact on the image sharpness. Images of extended uniform 68Ge sources, corrected for sensitivity and for the artifacts due detector dead spaces, have good uniformity. First clinical breast images are presented.

Assessment of DOI resolution in a fully mounted PEM scanner

The ClearPEM scanner is a dedicated system to perform breast imaging with the ability of measuring DOI, allowing an image spatial resolution close to 1.5 mm. The DOI is measured by calculating the amplitude asymmetry between the signals produced by two APD, one in the top and other in the bottom of the crystal. The DOI resolution measured in laboratory tests is 2.0 mm. In this paper we present a method to periodically confirm this value with the scanner fully mounted. The DOI resolution obtained with this method was 2.8 mm, which is consistent with the resolution measured during the laboratory tests.

ClearPEM scanners: Performance results and studies in preclinical environment

The ClearPEM detector is a dual planar Positron Emission Mammography (PEM) scanner that was developed within the framework of the international Crystal Clear Collaboration at CERN. The scanner is being used for preclinical studies and the new phase of the clinical trials will start on the second half of November. A second prototype was build and installed (ClearPEM-Sonic). The main results presented in this paper were obtained with the first prototype. The scanner image performance was evaluated using gelatin phantoms. The methodology included the quantification of the homogeneity (BV) and statistical noise (COV). Lesion detectability was evaluated using parameters such as lesion to background noise (LTBN) and lesion contrast recovery coefficient (CRC). Results indicate BV and COV of the order of 5-9% and 20-24%, respectively. ClearPEM images have been found globally homogeneous showing no artifacts. Small lesion to background ratio (LTB) and lesions of dimensions smaller than 3 mm showed less good contrast, but in most cases we report CRC values between 80% and 100%. The detection of lesions is feasible down to 2-3 mm in diameter.

Choosing the ART relaxation parameter for Clear-PEM 2D image reconstruction

The Algebraic Reconstruction Technique (ART) is an iterative image reconstruction algorithm. During the development of the Clear-PEM device, a PET scanner designed for the evaluation of breast cancer, multiple tests were done in order to optimise the reconstruction process. The comparison between ART, MLEM and OSEM indicates that ART can perform faster and with better image quality than the other, most common algorithms. It is claimed in this paper that if ARTs relaxation parameter is carefully adjusted to the reconstruction procedure it can produce high quality images in short computational time. This is confirmed by showing that with the relaxation parameter evolving as a logarithmic function, ART can match in terms of image quality and overcome in terms of computational time the performance of MLEM and OSEM algorithms. However, this study was performed only with simulated data and the level of noise with real data may be different.

First experimental results with the Clear-PEM detector

First experimental results of the imaging system Clear-PEM for positron emission mammography, under development within the framework of the Crystal Clear Collaboration at CERN, are presented. The quality control procedures of crystal pixels, APD arrays and assembled detector modules are described. The detector module performance was characterized in detail. Results on measurements of light yield, energy resolution, depth-of-interaction and inter-channel cross-talk are discussed. The status of the development of the front-end electronics and of the data acquisition boards is reported.