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.