Computational Image Analysis For Axonal Transport, Phenotypic Profiling, And Digital Pathology

Recent advances in fluorescent probes, microscopy, and imaging platforms have revolutionized biology and medicine, generating multi-dimensional image datasets at unprecedented scales. Traditional, low-throughput methods of image analysis are inadequate to handle the increased “volume, velocity, and variety” that characterize the realm of big data. Thus, biomedical imaging requires a new set of tools, which include advanced computer vision and machine learning algorithms. In this work, we develop computational image analysis solutions to biological questions at the level of single-molecules, cells, and tissues. At the molecular level, we dissect the regulation of dynein-dynactin transport initiation using in vitro reconstitution, single-particle tracking, super-resolution microscopy, live-cell imaging in neurons, and computational modeling. We show that at least two mechanisms regulate dynein transport initiation neurons: (1) cytoplasmic linker proteins, which are regulated by phosphorylation, increase the capture radius around the microtubule, thus reducing the time cargo spends in a diffusive search; and (2) a spatial gradient of tyrosinated alpha-tubulin enriched in the distal axon increases the affinity of dynein-dynactin for microtubules. Together, these mechanisms support a multi-modal recruitment model where interacting layers of regulation provide efficient, robust, and spatiotemporal control of transport initiation. At the cellular level, we develop and train deep residual convolutional neural networks on a large and diverse set of cellular microscopy images. Then, we apply networks trained for one task as deep feature extractors for unsupervised phenotypic profiling in a different task. We show that neural networks trained on one dataset encode robust image phenotypes that are sufficient to cluster subcellular structures by type and separate drug compounds by the mechanism of action, without additional training, supporting the strength and flexibility of this approach. Future applications include phenotypic profiling in image-based screens, where clustering genetic or drug treatments by image phenotypes may reveal novel relationships among genetic or pharmacologic pathways. Finally, at the tissue level, we apply deep learning pipelines in digital pathology to segment cardiac tissue and classify clinical heart failure using whole-slide images of cardiac histopathology. Together, these results demonstrate the power and promise of computational image analysis, computer vision, and deep learning in biological image analysis

Computing Interpretable Representations of Cell Morphodynamics

Shape changes (morphodynamics) are one of the principal ways cells interact with their environments and perform key intrinsic behaviours like division. These dynamics arise from a myriad of complex signalling pathways that often organise with emergent simplicity to carry out critical functions including predation, collaboration and migration. A powerful method for analysis can therefore be to quantify this emergent structure, bypassing the low-level complexity. Enormous image datasets are now available to mine. However, it can be difficult to uncover interpretable representations of the global organisation of these heterogeneous dynamic processes. Here, such representations were developed for interpreting morphodynamics in two key areas: mode of action (MoA) comparison for drug discovery (developed using the economically devastating Asian soybean rust crop pathogen) and 3D migration of immune system T cells through extracellular matrices (ECMs). For MoA comparison, population development over a 2D space of shapes (morphospace) was described using two models with condition-dependent parameters: a top-down model of diffusive development over Waddington-type landscapes, and a bottom-up model of tip growth. A variety of landscapes were discovered, describing phenotype transitions during growth, and possible perturbations in the tip growth machinery that cause this variation were identified. For interpreting T cell migration, a new 3D shape descriptor that incorporates key polarisation information was developed, revealing low-dimensionality of shape, and the distinct morphodynamics of run-and-stop modes that emerge at minute timescales were mapped. Periodically oscillating morphodynamics that include retrograde deformation flows were found to underlie active translocation (run mode). Overall, it was found that highly interpretable representations could be uncovered while still leveraging the enormous discovery power of deep learning algorithms. The results show that whole-cell morphodynamics can be a convenient and powerful place to search for structure, with potentially life-saving applications in medicine and biocide discovery as well as immunotherapeutics.Open Acces

Image analysis platforms for exploring genetic and neuronal mechanisms regulating animal behavior

An important aim of neuroscience is to understand how gene interactions and neuronal networks regulate animal behavior. The larvae of the marine annelid Platynereis dumerilii provide a convenient system for such integrative studies. These larvae exhibit a wide range of behaviors, including phototaxis, chemotaxis and gravitaxis and at the same time exhibit relatively simple nervous system organization. Due to its small size and transparent body, the Platynereis larva is compatible with whole-body light microscopic imaging following tissue staining protocols. It is also suitable for serial electron microscopic imaging and subsequent neuronal connectome reconstruction. Despite advances in imaging techniques, automated computational tools for large data analysis are not well-established in Platynereis. In the current work, I developed image analysis software for exploring genetic and nervous system mechanisms modulating Platynereis behavior. Exploring gene expression patterns Current labeling and imaging techniques restrict the number of gene expression patterns that can be labelled and visualized in a single specimen, which hinders the study of behaviors driven by multi-molecular interactions. To address this problem, I employed image registration to generate a gene expression atlas that integrates gene expression information from multiple specimens in a common reference space. The gene expression atlas was used to investigate mechanisms regulating larval locomotion, settlement and phototaxis in Platynereis. The atlas can assist in the identification of inter-individual and inter-species variations in gene expression. To provide a representation convenient for exploring gene expression patterns, I created a model of the atlas using 3D graphics software, which enabled convenient data visualization and efficient data storage and sharing. Exploring neuronal networks regulating behavior Neuronal circuitry can be reconstructed from the images obtained from electron microscopy, which resolves very fine structures such as neuron morphology or synapses. The amount of data resulting from electron microscopy and the complexity of neuronal networks represent a significant challenge for manual analysis. To solve this problem, I developed the NeuroDetective software, which models a neuronal circuitry and analyzes the information flow within it. The software combines the advantages of 3D visualization and graph analysis software by integrating neuron morphology and spatial distribution together with synaptic connectivity. NeuroDetective allowed studying the neuronal circuitry responsible for phototaxis in Platynereis larvae, revealing the connections and the neurons important for the network functionality. NeuroDetective facilitated the establishment of a relationship between the function and the structure of the neuronal circuitry in Platynereis phototaxis. Integrating gene expression patterns with neuronal connectivity Neuronal circuitry and its associated modulating biomolecules, such as neurotransmitters and neuropeptides, are thought to be the main factors regulating animal behavior. Therefore it was important to integrate both genetic and neuronal information in order to fully understand how biomolecules in conjunction with neuronal anatomy elicit certain animal behavior. To resolve the difference in specimen preparation for gene expression versus electron microscopy preparations, I developed an image registration procedure to match the signals from these two different datasets. This method enabled the integration the spatial distribution of specific modulators into the analysis of neuronal networks, leading to an improved understanding of the genetic and neuronal mechanisms modulating behavior in Platynereis

Honey Bee Health

Over the past decade, the worldwide decline in honey bee populations has been an important issue due to its implications for beekeeping and honey production. Honey bee pathologies are continuously studied by researchers, in order to investigate the host–parasite relationship and its effect on honey bee colonies. For these reasons, the interest of the veterinary community towards this issue has increased recently, and honey bee health has also become a subject of public interest. Bacteria, such as Melissococcus plutonius and Paenibacillus larvae, microsporidia, such as Nosema apis and Nosema ceranae, fungi, such as Ascosphaera apis, mites, such as Varroa destructor, predatory wasps, including Vespa velutina, and invasive beetles, such as Aethina tumida, are “old” and “new” subjects of important veterinary interest. Recently, the role of host–pathogen interactions in bee health has been included in a multifactorial approach to the study of these insects’ health, which involves a dynamic balance among a range of threats and resources interacting at multiple levels. The aim of this Special Issue is to explore honey bee health through a series of research articles that are focused on different aspects of honey bee health at different levels, including molecular health, microbial health, population genetic health, and the interaction between invasive species that live in strict contact with honey bee populations