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Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. We focus here on computational methods that promise to boost live-cell fluorescence microscopy,…

Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is…

Medical imaging informatics is a rapidly growing field that combines the principles of medical imaging and informatics to improve the acquisition, management, and interpretation of medical images. This chapter introduces the basic concepts…

Advances in digitizing tissue slides and the fast-paced progress in artificial intelligence, including deep learning, have boosted the field of computational pathology. This field holds tremendous potential to automate clinical diagnosis,…

Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…

As computer vision algorithms increase in capability, their applications in clinical systems will become more pervasive. These applications include: diagnostics, such as colonoscopy and bronchoscopy; guiding biopsies, minimally invasive…

Visualisation facilitates the understanding of scientific data both through exploration and explanation of visualised data. Provenance contributes to the understanding of data by containing the contributing factors behind a result. With the…

Luminescence imaging is invaluable for studying biological and material systems, particularly when advanced protocols that exploit temporal dynamics are employed. However, implementing such protocols often requires custom instrumentation,…

The past decade has witnessed a dramatic increase in the size and scope of biological and behavioral experiments. These experiments are providing an unprecedented level of detail and depth of data. However, this increase in data presents…

Over the last ten years, developments in whole-brain microscopy now allow for high-resolution imaging of intact brains of small rodents such as mice. These complex images contain a wealth of information, but many neuroscience laboratories…

The need for remote tools for healthcare monitoring has never been more apparent. Camera measurement of vital signs leverages imaging devices to compute physiological changes by analyzing images of the human body. Building on advances in…

Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…

Microscopy, in particular scanning probe and electron microscopy, has been pivotal in improving our understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most research characterization labs and…

Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…

Optical imaging of the brain has expanded dramatically in the past two decades. New optics, indicators, and experimental paradigms are now enabling in-vivo imaging from the synaptic to the cortex-wide scales. To match the resulting flood of…

Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…

Recently developed methods for video analysis, especially models for pose estimation and behavior classification, are transforming behavioral quantification to be more precise, scalable, and reproducible in fields such as neuroscience and…

Data sharing is a key factor for ensuring reproducibility and transparency of scientific experiments, and neuroimaging is no exception. The vast heterogeneity of data formats and imaging modalities utilised in the field makes it a very…

Microscopes have morphed from purely optical instruments into motorized, robotic machines that form images on digital sensors rather than eyeballs. This continuing trend towards automation and digitization enables many new approaches to…