DeepD3, an open framework for automated quantification of dendritic spines.

Dendritic spines are the seat of most excitatory synapses in the brain, and a cellular structure considered central to learning, memory, and activity-dependent plasticity. The quantification of dendritic spines from light microscopy data is usually performed by humans in a painstaking and error-prone process. We found that human-to-human variability is substantial (inter-rater reliability 82.2±6.4%), raising concerns about the reproducibility of experiments and the validity of using human-annotated 'ground truth' as an evaluation method for computational approaches of spine identification. To address this, we present DeepD3, an open deep learning-based framework to robustly quantify dendritic spines in microscopy data in a fully automated fashion. DeepD3's neural networks have been trained on data from different sources and experimental conditions, annotated and segmented by multiple experts and they offer precise quantification of dendrites and dendritic spines. Importantly, these networks were validated in a number of datasets on varying acquisition modalities, species, anatomical locations and fluorescent indicators. The entire DeepD3 open framework, including the fully segmented training data, a benchmark that multiple experts have annotated, and the DeepD3 model zoo is fully available, addressing the lack of openly available datasets of dendritic spines while offering a ready-to-use, flexible, transparent, and reproducible spine quantification method.

Limited functional convergence of eye-specific inputs in the retinogeniculate pathway of the mouse.

Segregation of retinal ganglion cell (RGC) axons by type and eye of origin is considered a hallmark of dorsal lateral geniculate nucleus (dLGN) structure. However, recent anatomical studies have shown that neurons in mouse dLGN receive input from multiple RGC types of both retinae. Whether convergent input leads to relevant functional interactions is unclear. We studied functional eye-specific retinogeniculate convergence using dual-color optogenetics in vitro. dLGN neurons were strongly dominated by input from one eye. Most neurons received detectable input from the non-dominant eye, but this input was weak, with a prominently reduced AMPAR:NMDAR ratio. Consistent with this, only a small fraction of thalamocortical neurons was binocular in vivo across visual stimuli and cortical projection layers. Anatomical overlap between RGC axons and dLGN neuron dendrites alone did not explain the strong bias toward monocularity. We conclude that functional eye-specific input selection and refinement limit convergent interactions in dLGN, favoring monocularity.

Soliton microcomb based spectral domain optical coherence tomography.

Spectral domain optical coherence tomography (OCT) is a widely employed, minimally invasive bio-medical imaging technique, which requires a broadband light source, typically implemented by super-luminescent diodes. Recent advances in soliton based photonic integrated frequency combs (soliton microcombs) have enabled the development of low-noise, broadband chipscale frequency comb sources, whose potential for OCT imaging has not yet been unexplored. Here, we explore the use of dissipative Kerr soliton microcombs in spectral domain OCT and show that, by using photonic chipscale Si3N4 resonators in conjunction with 1300 nm pump lasers, spectral bandwidths exceeding those of commercial OCT sources are possible. We characterized the exceptional noise properties of our source (in comparison to conventional OCT sources) and demonstrate that the soliton states in microresonators exhibit a residual intensity noise floor at high offset frequencies that is ca. 3 dB lower than a traditional OCT source at identical power, and can exhibit significantly lower noise performance for powers at the milli-Watt level. Moreover, we demonstrate that classical amplitude noise of all soliton comb teeth are correlated, i.e., common mode, in contrast to superluminescent diodes or incoherent microcomb states, which opens a new avenue to improve imaging speed and performance beyond the thermal noise limit.

Orthogonally polarized frequency comb generation from a Kerr comb via cross-phase modulation.

We experimentally demonstrate that a single microresonator can emit two orthogonally polarized individually coherent combs: (i) a strong polarized soliton comb and (ii) an orthogonally polarized continuous wave seeded weaker comb, generated from the first one via cross-phase modulation, sharing the repetition rate of the soliton comb. Experimental results show that the power of the transverse electric-polarized seed can be well below the threshold of comb generation (e.g., 0.1 mW). In addition, simulations show that a dark pulse could be generated in the anomalous dispersion regime by a bright soliton when the two orthogonally polarized modes have the same group velocity in the microresonator.

Second- and third-order nonlinear wavelength conversion in an all-optically poled Si3N4 waveguide.

Silicon nitride (Si3N4) is commonly employed to integrate third-order nonlinear optical processes on a chip. Its amorphous state, however, inhibits significant second-order nonlinear response. Recently, second-harmonic generation enhancement has been observed in Si3N4 waveguides after an all-optical poling (AOP) method. Here we demonstrate that, after AOP of a Si3N4 waveguide, for up to 2 W of coupled pump power, the same telecom-band signal undergoes larger interband wavelength conversion efficiency, based on sum-frequency generation (SFG), than intraband wavelength conversion, based on four-wave mixing. We also confirm the appearance of a phase-matching condition after AOP by measuring the conversion bandwidth and efficiency of SFG at different pump wavelengths.

Scalable and reconfigurable optical tapped-delay-line for multichannel equalization and correlation using nonlinear wave mixing and a Kerr frequency comb.

We experimentally demonstrate a scalable and reconfigurable optical tapped-delay-line (TDL) for multichannel equalization and correlation of 20-Gbaud quadrature-phase-shift-keyed (QPSK) signals using nonlinear wave mixing and a microresonator Kerr frequency comb. The optical TDL mainly consists of two stages: one being a multicasting of the original signals in a periodically poled lithium niobate (PPLN) waveguide with Kerr comb lines functioning as mutually coherent pumps, while the other is a coherent multiplexing of the delayed and weighted signal replicas in a second PPLN. A two- or three-tap optical TDL is demonstrated to simultaneously equalize a distorted QPSK data signal, reducing the error vector magnitude (EVM) from 22.5% to either 19.9% or 18.2%, and search two- or three-symbol patterns on another QPSK signal.

Double inverse nanotapers for efficient light coupling to integrated photonic devices.

Efficient light coupling to integrated photonic devices is of key importance to a wide variety of applications. "Inverse nanotapers" are widely used, in which the waveguide width is reduced to match an incident mode. Here, we demonstrate novel "double inverse" tapers, in which we reduce both the waveguide height and width. We demonstrate >45% chip-through coupling efficiency for both the transverse electric and transverse magnetic polarizations in Si3N4 tapers of >500 nm width, in comparison to regular inverse tapers that necessitate <100 nm width. The double inverse tapers show polarization-independent coupling and allow the fabrication using photolithography, relevant for applications at near-infrared and visible wavelengths, e.g., supercontinuum and soliton microcomb generation.

Effects of erbium-doped fiber amplifier induced pump noise on soliton Kerr frequency combs for 64-quadrature amplitude modulation transmission.

We experimentally investigate the effects of erbium-doped fiber amplifier induced pump noise on soliton Kerr frequency combs for 64-quadrature amplitude modulation (QAM) transmission. We find that the optical carrier-to-noise ratios (OCNRs) of the comb lines across the C-band almost linearly depend on the pump OCNR and are similar for a constant input pump power and noise. For a specific three-soliton state, despite higher comb line power, there is no noticeable OCNR improvement compared to the single-soliton comb. When the ASE noise on the pump is varied by 10 dB in the stable single-soliton state, the comb linewidths remain relatively unchanged and similar to the pump linewidth. Furthermore, four lines of the single-soliton Kerr comb produced by a pump light at an OCNR larger than 52 dB are used as coherent light sources to transmit 20-Gbaud 64-QAM signals over a 25-km fiber with bit error rate below the forward-error correction threshold.

An optical-frequency synthesizer using integrated photonics.

Optical-frequency synthesizers, which generate frequency-stable light from a single microwave-frequency reference, are revolutionizing ultrafast science and metrology, but their size, power requirement and cost need to be reduced if they are to be more widely used. Integrated-photonics microchips can be used in high-coherence applications, such as data transmission 1 , highly optimized physical sensors 2 and harnessing quantum states 3 , to lower cost and increase efficiency and portability. Here we describe a method for synthesizing the absolute frequency of a lightwave signal, using integrated photonics to create a phase-coherent microwave-to-optical link. We use a heterogeneously integrated III-V/silicon tunable laser, which is guided by nonlinear frequency combs fabricated on separate silicon chips and pumped by off-chip lasers. The laser frequency output of our optical-frequency synthesizer can be programmed by a microwave clock across 4 terahertz near 1,550 nanometres (the telecommunications C-band) with 1 hertz resolution. Our measurements verify that the output of the synthesizer is exceptionally stable across this region (synthesis error of 7.7 × 10-15 or below). Any application of an optical-frequency source could benefit from the high-precision optical synthesis presented here. Leveraging high-volume semiconductor processing built around advanced materials could allow such low-cost, low-power and compact integrated-photonics devices to be widely used.

Photonic chip-based soliton frequency combs covering the biological imaging window.

Dissipative Kerr solitons (DKS) in optical microresonators provide a highly miniaturised, chip-integrated frequency comb source with unprecedentedly high repetition rates and spectral bandwidth. To date, such frequency comb sources have been successfully applied in the optical telecommunication band for dual-comb spectroscopy, coherent telecommunications, counting of optical frequencies and distance measurements. Yet, the range of applications could be significantly extended by operating in the near-infrared spectral domain, which is a prerequisite for biomedical and Raman imaging applications, and hosts commonly used optical atomic transitions. Here we show the operation of photonic-chip-based soliton Kerr combs driven with 1 micron laser light. By engineering the dispersion properties of a Si3N4 microring resonator, octave-spanning soliton Kerr combs extending to 776 nm are attained, thereby covering the optical biological imaging window. Moreover, we show that soliton states can be generated in normal group-velocity dispersion regions when exploiting mode hybridisation with other mode families.

Large second harmonic generation enhancement in Si3N4 waveguides by all-optically induced quasi-phase-matching.

Efficient second harmonic generation in integrated platforms is usually achieved by resonant structures, intermodal phase-matching or quasi-phase matching by periodically poling ferroelectric waveguides. However, in all these structures, it is impossible to reconfigure the phase-matching condition in an all-optical way. Here, we demonstrate that a Watt-level laser causes a periodic modification of the second-order susceptibility in a silicon nitride waveguide, allowing for quasi-phase-matching between the pump and second harmonic modes for arbitrary wavelengths inside the erbium band. The grating is long-term inscribed, and leads to a second harmonic generation enhancement of more than 30 dB. We estimate a χ (2) on the order of 0.3 pm/V, with a maximum conversion efficiency of 0.05% W-1. We explain the observed phenomenon with the coherent photogalvanic effect model, which correctly agrees with the retrieved experimental parameters.

Tunable insertion of multiple lines into a Kerr frequency comb using electro-optical modulators.

We experimentally insert a flexible number of electro-optical (EO) comb lines into a Kerr frequency comb via EO modulation and demonstrate the use of combined Kerr and EO combs as light sources in coherent communications. The number of EO lines inserted into the Kerr comb can be varied by changing the modulation frequency. Additionally, the inserted EO comb is found to have similar coherence to that of the Kerr comb, as indicated by their linewidths. The high coherence of both the Kerr and EO combs has further been demonstrated in a communication experiment in which the comb lines are encoded with 10 Gbaud quadrature phase-shift-keyed signals. The increased number of comb lines after EO modulation indicates the possibility of obtaining more data channels in optical communications.

Pump-linewidth-tolerant wavelength multicasting using soliton Kerr frequency combs.

We experimentally demonstrate pump-linewidth-tolerant wavelength multicasting using microresonator-based soliton Kerr frequency combs. When Kerr comb lines serve as coherent pumps in a periodically poled lithium niobate waveguide, the linewidth of the multicast signal almost remains that of the original signal at different linewidths of Kerr combs, ranging from 100 kHz to 1 MHz. However, in conventional multicasting where free-running (FR) pumps are used, the linewidth of the converted signal significantly increases. Furthermore, the error vector magnitude (EVM) performance demonstrates eight-fold error-free multicasting of 10 Gbaud 16-quadrature amplitude modulation signals, even when the linewidths of the Kerr combs are as broad as 1 MHz (no Kalman filtering algorithm in the receiver). In contrast, the EVM performance of the signal copy is degraded with an FR laser as a dummy pump.

Microresonator-based solitons for massively parallel coherent optical communications.

Solitons are waveforms that preserve their shape while propagating, as a result of a balance of dispersion and nonlinearity. Soliton-based data transmission schemes were investigated in the 1980s and showed promise as a way of overcoming the limitations imposed by dispersion of optical fibres. However, these approaches were later abandoned in favour of wavelength-division multiplexing schemes, which are easier to implement and offer improved scalability to higher data rates. Here we show that solitons could make a comeback in optical communications, not as a competitor but as a key element of massively parallel wavelength-division multiplexing. Instead of encoding data on the soliton pulse train itself, we use continuous-wave tones of the associated frequency comb as carriers for communication. Dissipative Kerr solitons (DKSs) (solitons that rely on a double balance of parametric gain and cavity loss, as well as dispersion and nonlinearity) are generated as continuously circulating pulses in an integrated silicon nitride microresonator via four-photon interactions mediated by the Kerr nonlinearity, leading to low-noise, spectrally smooth, broadband optical frequency combs. We use two interleaved DKS frequency combs to transmit a data stream of more than 50 terabits per second on 179 individual optical carriers that span the entire telecommunication C and L bands (centred around infrared telecommunication wavelengths of 1.55 micrometres). We also demonstrate coherent detection of a wavelength-division multiplexing data stream by using a pair of DKS frequency combs-one as a multi-wavelength light source at the transmitter and the other as the corresponding local oscillator at the receiver. This approach exploits the scalability of microresonator-based DKS frequency comb sources for massively parallel optical communications at both the transmitter and the receiver. Our results demonstrate the potential of these sources to replace the arrays of continuous-wave lasers that are currently used in high-speed communications. In combination with advanced spatial multiplexing schemes and highly integrated silicon photonic circuits, DKS frequency combs could bring chip-scale petabit-per-second transceivers into reach.

Dependence of a microresonator Kerr frequency comb on the pump linewidth.

We experimentally investigate the dependence of Kerr comb generation, comb linewidth, and coherent system performance on the pump linewidth in a microresonator. We find that the generation of the primary comb can have a larger tolerance to the pump linewidth compared with that of the low-phase-noise comb. In addition, the linewidths of the generated combs are almost linearly dependent on the pump linewidth in the primary and low-phase-noise states. Furthermore, the optical signal-to-noise ratio penalty between the pump and generated Kerr combs in a coherent communication system is less than 0.2 dB in both the primary and low-phase-noise states, showing that Kerr frequency combs in these two states can have similar coherent system performance to the pump.

Heterogeneous integration of lithium niobate and silicon nitride waveguides for wafer-scale photonic integrated circuits on silicon.

An ideal photonic integrated circuit for nonlinear photonic applications requires high optical nonlinearities and low loss. This work demonstrates a heterogeneous platform by bonding lithium niobate (LN) thin films onto a silicon nitride (Si3N4) waveguide layer on silicon. It not only provides large second- and third-order nonlinear coefficients, but also shows low propagation loss in both the Si3N4 and the LN-Si3N4 waveguides. The tapers enable low-loss-mode transitions between these two waveguides. This platform is essential for various on-chip applications, e.g., modulators, frequency conversions, and quantum communications.

Dual-pump generation of high-coherence primary Kerr combs with multiple sub-lines.

We experimentally generate high-coherence primary Kerr combs with multiple sub-lines by using dual pumps and demonstrate the application of a primary comb state in multichannel communications. We find that more than 10 primary comb lines can be generated within the spectrum of modulation instability gain in our microring resonator. The generation is also verified by numerical simulations and the measured linewidth confirms the high coherence of the generated primary comb lines. We also demonstrate the high-coherence characteristics in a coherent communication experiment, in which each comb line is encoded with 20 Gbaud quadrature phase-shift-keyed signals.

Bringing short-lived dissipative Kerr soliton states in microresonators into a steady state.

Dissipative Kerr solitons have recently been generated in optical microresonators, enabling ultrashort optical pulses at microwave repetition rates, that constitute coherent and numerically predictable Kerr frequency combs. However, the seeding and excitation of the temporal solitons is associated with changes in the intracavity power that can lead to large thermal resonance shifts and render the soliton states in most commonly used resonator platforms short lived. Here we describe a "power kicking" method to overcome this instability by modulating the power of the pump laser. With this method also initially very short-lived (of the order of 100 ns) soliton states can be brought into a steady state in contrast to techniques reported earlier which relied on an adjustment of the laser scan speed only. Once the soliton state is in a steady state it can persist for hours and is thermally self-locked.

Demonstration of optical multicasting using Kerr frequency comb lines.

We experimentally demonstrate optical multicasting using Kerr frequency combs generated from a Si3N4 microresonator. We obtain Kerr combs in two states with different noise properties by varying the pump wavelength in the resonator and investigate the effect of Kerr combs on multicasting. Seven-fold multicasting of 20 Gbaud quadrature phase-shift-keyed signals and four-fold multicasting of 16-quadrature amplitude modulation signals have been achieved when low-phase-noise combs are input into a periodically poled lithium niobate waveguide. In addition, we find that the wavelength conversion efficiency in the PPLN waveguide for chaotic combs with high noise is similar to that for low-noise combs, while the signal quality of the multicast copy is significantly degraded.

Frequency-comb-assisted broadband precision spectroscopy with cascaded diode lasers.

Frequency-comb-assisted diode laser spectroscopy, employing both the accuracy of an optical frequency comb and the broad wavelength tuning range of a tunable diode laser, has been widely used in many applications. In this Letter, we present a novel method using cascaded frequency agile diode lasers, which allows us to extend the measurement bandwidth to 37.4 THz (1355-1630 nm) at megahertz resolution with scanning speeds above 1 THz/s. It is demonstrated as a useful tool to characterize a broadband spectrum for molecular spectroscopy, and in particular it enables us to characterize the dispersion of integrated microresonators up to the 4th-order.