About
56
Publications
10,829
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
3,245
Citations
Introduction
Current institution
Additional affiliations
March 2011 - present
June 2002 - August 2005
April 1995 - May 2002
Education
September 1984 - August 1990
September 1982 - June 1984
September 1976 - June 1980
Publications
Publications (56)
The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for the segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (i) generality by reconstructing cell lineages in four-dimensional, terab...
OPTIMAL foraging theory is based on the assumption that natural selection favours animals that forage most efficiently1-3. But such selection does not act directly on foraging efficiency, but rather indirectly by favouring animals that survive and reproduce most successfully. Studies that use optimal foraging models often assume that maximization o...
The experiments presented here were designed to determine the origin of the temporally complex activity of antennal lobe projection neurons in the cockroach olfactory system. We determined this through the use of complex chemical stimuli that evoked neural activity recorded extracellularly from olfactory sensory neurons and intracellularly from ant...
A subset of Drosophila neurons that expresses crustacean cardioactive peptide (CCAP) has been shown previously to make the hormone bursicon, which is required for cuticle tanning and wing expansion after eclosion. Here we present evidence that CCAP-expressing neurons (NCCAP) consist of two functionally distinct groups, one of which releases bursico...
Coupling of autonomous cellular oscillators is an essential aspect of circadian clock function but little is known about its circuit requirements. Functional ablation of the pigment-dispersing factor-expressing lateral ventral subset (LNV) of Drosophila clock neurons abolishes circadian rhythms of locomotor activity. The hypothesis that LNVs synchr...
Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright d...
Genetically encoded fluorescent calcium indicators have revolutionized neuroscience and other biological fields by allowing cellular-resolution recording of physiology during behavior. However, we currently lack bright, genetically targetable indicators in the near infrared that can be used in animals. Here, we describe WHaloCaMP, a modular chemige...
We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8% of cell lineages spanning 1 h, as compared to 31.8% for the competing method. Our approach improves understanding of whe...
We present a method for automated nucleus identification and tracking in time-lapse microscopy recordings of entire developing embryos. Our method combines deep learning and global optimization to enable complete lineage reconstruction from sparse point annotations, and uses parallelization to process multi-terabyte light-sheet recordings, which we...
Glucose is arguably the most important molecule in metabolism, and its dysregulation underlies diabetes. We describe a family of single-wavelength genetically encoded glucose sensors with a high signal-to-noise ratio, fast kinetics, and affinities varying over four orders of magnitude (1 μM to 10 mM). The sensors allow mechanistic characterization...
At the time of this writing, searching Google Scholar for ‘light-sheet microscopy’ returns almost 8500 results; over three-quarters of which were published in the last 5 years alone. Searching for other advanced imaging methods in the last 5 years yields similar results: ‘super-resolution microscopy’ (>16 000), ‘single-molecule imaging’ (almost 10...
Glucose is arguably the most important molecule in metabolism, and its mismanagement underlies diseases of vast societal import, most notably diabetes. Although glucose-related metabolism has been the subject of intense study for over a century, tools to track glucose in living organisms with high spatio-temporal resolution are lacking. We describe...
The thirteen nuclear cleavages that give rise to the Drosophila blastoderm are some of the fastest known cell cycles [1]. Surprisingly, the fertilized egg is provided with at most one-third of the dNTPs needed to complete the thirteen rounds of DNA replication [2]. The rest must be synthesized by the embryo, concurrent with cleavage divisions. What...
We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detection focal planes in living speci...
Mechanics plays a key role in the development of higher organisms. However, understanding this relationship is complicated by the difficulty of modeling the link between local forces generated at the subcellular level and deformations observed at the tissue and whole-embryo levels. Here we propose an approach first developed for lipid bilayers and...
Pushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the Janelia Fluor (JF) series of dyes....
A BSTRACT
Pushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the ‘Janelia Fluor’ (JF) seri...
Optimal image quality in light-sheet microscopy requires a perfect overlap between the illuminating light sheet and the focal plane of the detection objective. However, mismatches between the light-sheet and detection planes are common owing to the spatiotemporally varying optical properties of living specimens. Here we present the AutoPilot framew...
We developed isotropic multiview (IsoView) light-sheet microscopy in order to image fast cellular dynamics, such as cell movements in an entire developing embryo or neuronal activity throughput an entire brain or nervous system, with high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To achieve high...
We present the Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. RACE is 55–330 times faster and 2–5 times more accurate than state-of-the-art methods. We demonstrate the generality of RACE by extracting cell-shape information from enti...
Imaging fast cellular dynamics across large specimens requires high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To meet these requirements, we developed isotropic multiview (IsoView) light-sheet microscopy, which rapidly images large specimens via simultaneous light-sheet illumination and fluoresc...
Mechanics plays a key role in the development of higher organisms. However, working towards an understanding of this relationship is complicated by the fact that it has proven difficult to model the link between local forces generated at the subcellular level, and tissue deformation at the whole-embryo level. Here we propose an approach first devel...
Light-sheet microscopy is a powerful method for imaging the development and function of complex biological systems at high spatiotemporal resolution and over long time scales. Such experiments typically generate terabytes of multidimensional image data, and thus they demand efficient computational solutions for data management, processing and analy...
Understanding how the brain works in tight concert with the rest of the central nervous system (CNS) hinges upon knowledge of coordinated activity patterns across the whole CNS. We present a method for measuring activity in an entire, non-transparent CNS with high spatiotemporal resolution. We combine a light-sheet microscope capable of simultaneou...
Technical drawings of individual components and complete assemblies of custom four-axis stage and flexure systems in the hs-SiMView light-sheet microscope
Source code for processing multi-view functional imaging data, detecting and classifying fictive locomotor behaviors, and mapping activity timing across the central nervous system
Spatial resolution maps for the Drosophila 3rd instar larval CNS
Slice-by-slice image sequence of a three-dimensional image stack of a Drosophila 3rd instar larval CNS expressing the ubiquitous nuclear label His2Av-eGFP (left), as well as corresponding three-dimensional spatial resolution maps estimating lateral (middle) and axial (right) resolutio...
Supplementary Figures 1-8 and Supplementary Methods and Supplementary References
Spatial resolution maps for the Drosophila 2nd instar larval CNS
Slice-by-slice image sequence of a three-dimensional image stack of a Drosophila 2nd instar larval CNS expressing the ubiquitous nuclear label His2Av-eGFP (left), as well as corresponding three-dimensional spatial resolution maps estimating lateral (middle) and axial (right) resolutio...
Whole-CNS activity timing map for forward locomotor waves
Slice-by-slice image sequence of the three-dimensional whole-CNS activity timing map computed for fictive forward locomotor waves (n = 30). For clarity, timing data and the improvement in activity fit given time (referred to as “information gain” or “info. gain” for simplicity) are shown as...
Whole-CNS activity timing map for backward locomotor waves
Slice-by-slice visualization of the three-dimensional whole-CNS activity timing map as in Supplementary Movie 9, but for fictive backward locomotor waves (n = 70).
Whole-CNS functional imaging with two-photon multi-view lightsheet microscopy (raw data and ΔF/F)
Maximum-intensity projections of raw image data (left) and ΔF/F (right) for the two-photon Drosophila whole-CNS functional imaging experiment shown in Supplementary Movie 3. Image data shown to the left was background-corrected using a long-range Gauss...
Whole-CNS functional imaging with two-photon multi-view lightsheet microscopy (volume rendering)
Three-dimensional, rotating volume rendering of two backward wave sequences from the twophoton Drosophila whole-CNS functional imaging experiment shown in Supplementary Movie 3. The CNS anatomy shown in grey represents GCaMP6s baseline fluorescence, whi...
Spatial resolution maps for the Drosophila 1st instar larval CNS
Left: Slice-by-slice image sequence of a three-dimensional image stack of a Drosophila 1st instar larval CNS expressing the ubiquitous nuclear label His2Av-eGFP, recorded with our light-sheet microscope for multi-view functional imaging. Middle/right: Slice-by-slice image sequence of...
The fruit fly is an excellent model system for investigating the sequence of epithelial tissue invaginations constituting the process of gastrulation. By combining recent advancements in light sheet fluorescence microscopy (LSFM) and image processing, the three-dimensional fly embryo morphology and relevant gene expression patterns can be accuratel...
Axonal branching allows a neuron to connect to several targets, increasing neuronal circuit complexity. While axonal branching is well described, the mechanisms that control it remain largely unknown. We find that in the Drosophila CNS branches develop through a process of excessive growth followed by pruning. In vivo high-resolution live imaging o...
In vivo imaging applications typically require carefully balancing conflicting parameters. Often it is necessary to achieve high imaging speed, low photo-bleaching and photo-toxicity, good three-dimensional resolution, high signal-to-noise ratio, and excellent physical coverage at the same time. Light-sheet microscopy provides good performance in a...
We report a new fabrication technique for realizing a high-density penetrating metal microelectrode array intended for acute multiple-unit neural recordings. The microelectrode array consists of multiple metal shanks projecting from a silicon supporting bulk. Neural recording sites, separated by an average spacing of 50 μm, are located at the tip o...
Here we consider the issue of choice and how neural systems can be used to investigate the processes of discrimination, as well as the evolution of different kinds of choice-related behavior in animals. We develop these ideas in the context of three studies, among others. The first study is on the evolution of specialization in animals using locust...
Insects attempting to identify and classify general, food-related odors in a natural environment are faced with the difficult problem of turning a spatially and temporally noisy, multicomponent olfactory stimulus into a reliable neural code that is independent of spurious changes in concentration or the temporal structure of the odor plume. The ins...
Behavioral evidence indicates that insects preferentially orient toward pulses of odorants as they occur downwind from a point source. Our recent results have shown that cockroach olfactory receptor neurons are able to reliably resolve 10-Hz pulses of the general "green' odorant 1-hexanol, but it is unknown to what extent the central olfactory path...
During the metamorphosis of Manduca sexta the larval nervous system is reorganized to allow the generation of behaviors that are specific to the pupal and adult stages. In some instances, metamorphic changes in neurons that persist from the larval stage are segment-specific and lead to expression of segment-specific behavior in later stages. At the...
Stimulation of sensory neurons innervating hairs in the gin traps on the abdomen of Manduca sexta pupae evokes a rapid bending of the abdomen that is restricted to one or more of the three articulating posterior segments. However, electrical stimulation of the gin trap sensory nerve in an isolated abdominal nerve cord evokes characteristic motor ne...
Behavioral and physiological evidence indicates that insect pheromone sensory neurons are able to resolve pulses of pheromone concentration as they occur downwind from a point source, but the abilities of insect sensory neurons that are sensitive to general odors to respond to pulsatile stimuli are unknown. The temporal response characteristics of...
Recent studies that have shown that variation in avian foraging behavior can produce changes in reproductive success and survival have raised the question of the role of energy budgets in determining reproductive behavior and other life-history traits of birds. The study reported here describes how the daily energy budgets of breeding populations o...
I measured the heritability of foraging patch choice in a laboratory population of zebra finches (Taeniopygia guttata). Mothers and offspring were tested for their ability to discriminate between four foraging patches which provided four different rates of energy gain. Use of a foraging patch with a high rate of energy gain has been shown to confer...
The critical assumption of optimal foraging theory is that foragers with high net rates of energy gain have higher fitness than foragers with low net rates of energy gain. To test this assumption 60 pairs of zebra finches, Taeniopygia guttata, were randomly assigned to four experimental treatments in which their rate of energy gain was altered by i...
A classical conditioning paradigm was used to test the ability of Sternopygus macrurus to detect EOD-like stimuli (sine waves) of different frequencies. The behavioral tuning curves were quite close in shape to tuning curves based on single-unit recordings of T units, although the sensitivity at all frequencies was much greater. The behavioral curv...
A classical conditioning paradigm was used to test the ability of Sternopygus macrurus to detect EOD-like stimuli (sine waves) of different frequencies. The behavioral tuning curves were quite close in shape to tuning curves based on single-unit recordings of T units, although the sensitivity at all frequencies was much greater. The behavioral curv...
