Rethinking Timing Residuals: Advancing PET Detectors with Explicit TOF Corrections

PET is a functional imaging method that visualizes metabolic processes. TOF information can be derived from coincident detector signals and incorporated into image reconstruction to enhance the SNR. PET detectors are typically assessed by their CTR, but timing performance is degraded by various factors. Research on timing calibration seeks to mitigate these degradations and restore accurate timing information. While many calibration methods use analytical approaches, machine learning techniques have recently gained attention due to their flexibility. We developed a residual physics-based calibration approach that combines prior domain knowledge with the power of machine learning models. This approach begins with an initial analytical calibration addressing first-order skews. The remaining deviations, regarded as residual effects, are used to train machine learning models to eliminate higher-order skews. The key advantage is that the experimenter guides the learning process through the definition of timing residuals. In earlier studies, we developed models that directly predicted the expected time difference, which offered corrections only implicitly (implicit correction models). In this study, we introduce a new definition for timing residuals, enabling us to train models that directly predict correction values (explicit correction models). The explicit correction approach significantly simplifies data acquisition, improves linearity, and enhances timing performance from $371 \pm 6$ ps to $281 \pm 5$ ps for coincidences from 430 keV to 590 keV. Additionally, the new definition reduces model size, making it suitable for high-throughput applications like PET scanners. Experiments were conducted using two detector stacks composed of $4 \times 4$ LYSO:Ce,Ca crystals ($3.8\times 3.8\times 20$ mm$^{3}$) coupled to $4 \times 4$ Broadcom NUV-MT SiPMs and digitized with the TOFPET2 ASIC.

PointFISH -- learning point cloud representations for RNA localization patterns

Subcellular RNA localization is a critical mechanism for the spatial control of gene expression. Its mechanism and precise functional role is not yet very well understood. Single Molecule Fluorescence in Situ Hybridization (smFISH) images allow for the detection of individual RNA molecules with subcellular accuracy. In return, smFISH requires robust methods to quantify and classify RNA spatial distribution. Here, we present PointFISH, a novel computational approach for the recognition of RNA localization patterns. PointFISH is an attention-based network for computing continuous vector representations of RNA point clouds. Trained on simulations only, it can directly process extracted coordinates from experimental smFISH images. The resulting embedding allows scalable and flexible spatial transcriptomics analysis and matches performance of hand-crafted pipelines.

Improving the Timing Resolution of Positron Emission Tomography Detectors using Boosted Learning -- A Residual Physics Approach

Artificial intelligence is finding its way into medical imaging, usually focusing on image reconstruction or enhancing analytical reconstructed images. However, optimizations along the complete processing chain, from detecting signals to computing data, enable significant improvements. Thus, we present an approach toward detector optimization using boosted learning by exploiting the concept of residual physics. In our work, we improve the coincidence time resolution (CTR) of positron emission tomography (PET) detectors. PET enables imaging of metabolic processes by detecting {\gamma}-photons with scintillation detectors. Current research exploits light-sharing detectors, where the scintillation light is distributed over and digitized by an array of readout channels. While these detectors demonstrate excellent performance parameters, e.g., regarding spatial resolution, extracting precise timing information for time-of-flight (TOF) becomes more challenging due to deteriorating effects called time skews. Conventional correction methods mainly rely on analytical formulations, theoretically capable of covering all time skew effects, e.g., caused by signal runtimes or physical effects. However, additional effects are involved for light-sharing detectors, so finding suitable analytical formulations can become arbitrarily complicated. The residual physics-based strategy uses gradient tree boosting (GTB) and a physics-informed data generation mimicking an actual imaging process by shifting a radiation source. We used clinically relevant detectors with a height of 19 mm, coupled to digital photosensor arrays. All trained models improved the CTR significantly. Using the best model, we achieved CTRs down to 198 ps (185 ps) for energies ranging from 300 keV to 700 keV (450 keV to 550 keV).

ImJoy: an open-source computational platform for the deep learning era

Deep learning methods have shown extraordinary potential for analyzing very diverse biomedical data, but their dissemination beyond developers is hindered by important computational hurdles. We introduce ImJoy (https://imjoy.io/), a flexible and open-source browser-based platform designed to facilitate widespread reuse of deep learning solutions in biomedical research. We highlight ImJoy's main features and illustrate its functionalities with deep learning plugins for mobile and interactive image analysis and genomics.