A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice.

Advances in head-mounted microscopes have enabled imaging of neuronal activity using genetic tools in freely moving mice but these microscopes are restricted to recording in minimally lit arenas and imaging upper cortical layers. Here we built a 2-g, three-photon excitation-based microscope, containing a z-drive that enabled access to all cortical layers while mice freely behaved in a fully lit environment. The microscope had on-board photon detectors, robust to environmental light, and the arena lighting was timed to the end of each line-scan, enabling functional imaging of activity from cortical layer 4 and layer 6 neurons expressing jGCaMP7f in mice roaming a fully lit or dark arena. By comparing the neuronal activity measured from populations in these layers we show that activity in cortical layer 4 and layer 6 is differentially modulated by lit and dark conditions during free exploration.

Estimation of skeletal kinematics in freely moving rodents.

Forming a complete picture of the relationship between neural activity and skeletal kinematics requires quantification of skeletal joint biomechanics during free behavior; however, without detailed knowledge of the underlying skeletal motion, inferring limb kinematics using surface-tracking approaches is difficult, especially for animals where the relationship between the surface and underlying skeleton changes during motion. Here we developed a videography-based method enabling detailed three-dimensional kinematic quantification of an anatomically defined skeleton in untethered freely behaving rats and mice. This skeleton-based model was constrained using anatomical principles and joint motion limits and provided skeletal pose estimates for a range of body sizes, even when limbs were occluded. Model-inferred limb positions and joint kinematics during gait and gap-crossing behaviors were verified by direct measurement of either limb placement or limb kinematics using inertial measurement units. Together we show that complex decision-making behaviors can be accurately reconstructed at the level of skeletal kinematics using our anatomically constrained model.

Three-photon head-mounted microscope for imaging deep cortical layers in freely moving rats.

We designed a head-mounted three-photon microscope for imaging deep cortical layer neuronal activity in a freely moving rat. Delivery of high-energy excitation pulses at 1,320 nm required both a hollow-core fiber whose transmission properties did not change with fiber movement and dispersion compensation. These developments enabled imaging at >1.1 mm below the cortical surface and stable imaging of layer 5 neuronal activity for >1 h in freely moving rats performing a range of behaviors.

Optical Riblet Sensor: Beam Parameter Requirements for the Probing Laser Source.

Beam parameters of a probing laser source in an optical riblet sensor are studied by considering the high demands on a sensors' precision and reliability for the determination of deviations of the geometrical shape of a riblet. Mandatory requirements, such as minimum intensity and light polarization, are obtained by means of detailed inspection of the optical response of the riblet using ray and wave optics; the impact of wavelength is studied. Novel measures for analyzing the riblet shape without the necessity of a measurement with a reference sample are derived; reference values for an ideal riblet structure obtained with the optical riblet sensor are given. The application of a low-cost, frequency-doubled Nd:YVO4 laser pointer sufficient to serve as a reliable laser source in an appropriate optical riblet sensor is discussed.

Explaining the success of Kogelnik's coupled-wave theory by means of perturbation analysis: discussion.

The problem of diffraction of an electromagnetic wave by a thick hologram grating can be solved by the famous Kogelnik's coupled-wave theory (CWT) to a very high degree of accuracy. We confirm this finding by comparing the CWT and the exact result for a typical example and propose an explanation in terms of perturbation theory. To this end we formulate the problem of diffraction as a matrix problem following similar well-known approaches, especially rigorous coupled-wave theory (RCWT). We allow for a complex permittivity modulation and a possible phase shift between refractive index and absorption grating and explicitly incorporate appropriate boundary conditions. The problem is solved numerically exact for the specific case of a planar unslanted grating and a set of realistic values of the material's parameters and experimental conditions. Analogously, the same problem is solved for a two-dimensional truncation of the underlying matrix that would correspond to a CWT approximation but without the usual further approximations. We verify a close coincidence of both results even in the off-Bragg region and explain this result by means of a perturbation analysis of the underlying matrix problem. Moreover, the CWT is found not only to coincide with the perturbational approximation in the in-Bragg and the extreme off-Bragg cases, but also to interpolate between these extremal regimes.

Connectomic analysis of thalamus-driven disinhibition in cortical layer 4.

Sensory signals are transmitted via the thalamus primarily to layer 4 (L4) of the primary sensory cortices. While information about average neuronal connectivity in L4 is available, its detailed higher-order circuit structure is not known. Here, we used three-dimensional electron microscopy for a connectomic analysis of the thalamus-driven inhibitory network in L4. We find that thalamic input drives a subset of interneurons with high specificity, which in turn target excitatory neurons with subtype specificity. These interneurons create a directed disinhibitory network directly driven by the thalamic input. Neuronal activity recordings show that strong synchronous sensory activation yields about 1.5-fold stronger activation of star pyramidal cells than spiny stellates, in line with differential windows of opportunity for activation of excitatory neurons in the thalamus-driven disinhibitory circuit model. With this, we have identified a high degree of specialization of the microcircuitry in L4 of the primary sensory cortex.

Visual pursuit behavior in mice maintains the pursued prey on the retinal region with least optic flow.

Mice have a large visual field that is constantly stabilized by vestibular ocular reflex (VOR) driven eye rotations that counter head-rotations. While maintaining their extensive visual coverage is advantageous for predator detection, mice also track and capture prey using vision. However, in the freely moving animal quantifying object location in the field of view is challenging. Here, we developed a method to digitally reconstruct and quantify the visual scene of freely moving mice performing a visually based prey capture task. By isolating the visual sense and combining a mouse eye optic model with the head and eye rotations, the detailed reconstruction of the digital environment and retinal features were projected onto the corneal surface for comparison, and updated throughout the behavior. By quantifying the spatial location of objects in the visual scene and their motion throughout the behavior, we show that the prey image consistently falls within a small area of the VOR-stabilized visual field. This functional focus coincides with the region of minimal optic flow within the visual field and consequently area of minimal motion-induced image-blur, as during pursuit mice ran directly toward the prey. The functional focus lies in the upper-temporal part of the retina and coincides with the reported high density-region of Alpha-ON sustained retinal ganglion cells.

Mice have a lot to keep an eye on. To survive, they need to dodge predators looming on land and from the skies, while also hunting down the small insects that are part of their diet. To do this, they are helped by their large panoramic field of vision, which stretches from behind and over their heads to below their snouts. To stabilize their gaze when they are on the prowl, mice reflexively move their eyes to counter the movement of their head: in fact, they are unable to move their eyes independently. This raises the question: what part of their large visual field of view do these rodents use when tracking a prey, and to what advantage? This is difficult to investigate, since it requires simultaneously measuring the eye and head movements of mice as they chase and capture insects. In response, Holmgren, Stahr et al. developed a new technique to record the precise eye positions, head rotations and prey location of mice hunting crickets in surroundings that were fully digitized at high resolution. Combining this information allowed the team to mathematically recreate what mice would see as they chased the insects, and to assess what part of their large visual field they were using. This revealed that, once a cricket had entered any part of the mice's large field of view, the rodents shifted their head ­ but not their eyes ­ to bring the prey into both eye views, and then ran directly at it. If the insect escaped, the mice repeated that behavior. During the pursuit, the cricket's position was mainly held in a small area of the mouse's view that corresponds to a specialized region in the eye which is thought to help track objects. This region also allowed the least motion-induced image blur when the animals were running forward. The approach developed by Holmgren, Stahr et al. gives a direct insight into what animals see when they hunt, and how this constantly changing view ties to what happens in the eyes. This method could be applied to other species, ushering in a new wave of tools to explore what freely moving animals see, and the relationship between behaviour and neural circuitry.

Interference and holography with femtosecond laser pulses of different colours.

Interferometry and holography are two domains that are based on observation and recording of interference fringes from two light beams. While the aim of the first technique is to reveal and map the phase difference of two wave fronts, the main task of the second technique is to reconstruct one of the two recording waves via diffraction of the other wave from the recorded fringe pattern (hologram). To create fringes, mutually coherent waves from the same laser are commonly used. It is shown here that fringes can be observed and holograms can be recorded with ultrashort, sub-picosecond pulses even of different colour, generated in our experiment with two parametric amplifiers seeded, both by the same mode-locked Ti-sapphire laser. The appearance of permanent and transient gratings is confirmed by recording of an image-bearing hologram, by observation of two-beam coupling gain in a pump-probe experiment and by frequency conversion in Raman-Nath self-diffraction from a moving grating.

Holographic Spectroscopy: Wavelength-Dependent Analysis of Photosensitive Materials by Means of Holographic Techniques.

Holographic spectroscopy is highlighted as a powerful tool for the analysis of photosensitive materials with pronounced alterations of the complex permittivity over a broad range in the visible spectrum, due to the advances made both in the fields of advanced holographic media and highly tunable lasers systems. To analytically discuss consequences for in- and off-Bragg reconstruction, we revised Kogelnik's coupled wave theory strictly on the basis of complex permittivities. We extended it to comply with modern experimental parameters such as out-of-phase mixed holograms and highly modulated gratings. A spatially modulated, wavelength-dependent permittivity that superimposes a spatially homogeneous wavelength-dependent ground state spectrum is taken into account for signal wave reconstruction with bulky elementary mixed gratings as an example. The dispersion characteristics of the respective diffraction efficiency is modelled for color-center-absorption and absorption of strongly localized carriers. As an example for the theoretical possibilities of our newly derived set of equations, we present a quantitative analysis of the Borrmann effect connected to out-of-phase gratings, providing easier and more intuitive methods for the derivation of their grating parameters.