Mammalian gene expression variability is explained by underlying cell state.

Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele-specific transcriptional bursting (intrinsic). Yet, the relative contribution of these two distinct sources is unknown. Here, we exploit the qualitative difference in the patterns of covariance between these two sources to quantify their relative contributions to expression variance in mammalian cells. Using multiplexed error robust RNA fluorescent in situ hybridization (MERFISH), we measured the multivariate gene expression distribution of 150 genes related to Ca2+ signaling coupled with the dynamic Ca2+ response of live cells to ATP. We show that after controlling for cellular phenotypic states such as size, cell cycle stage, and Ca2+ response to ATP, the remaining variability is effectively at the Poisson limit for most genes. These findings demonstrate that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal

Quaternary pulse position modulation electronics for free-space laser communications

The development of a high data-rate communications electronic subsystem for future application in free-space, direct-detection laser communications is described. The dual channel subsystem uses quaternary pulse position modulation (QPPM) and operates at a throughput of 650 megabits per second. Transmitting functions described include source data multiplexing, channel data multiplexing, and QPPM symbol encoding. Implementation of a prototype version in discrete gallium arsenide logic, radiofrequency components, and microstrip circuitry is presented

Optical orbital-angular-momentum-multiplexed data transmission under high scattering

Multiplexing multiple orbital angular momentum (OAM) channels enables high-capacity optical communication. However, optical scattering from ambient microparticles in the atmosphere or mode coupling in optical fibers significantly decreases the orthogonality between OAM channels for demultiplexing and eventually increases crosstalk in communication. Here, we propose a novel scattering-matrix-assisted retrieval technique (SMART) to demultiplex OAM channels from highly scattered optical fields and achieve an experimental crosstalk of –13.8 dB in the parallel sorting of 24 OAM channels after passing through a scattering medium. The SMART is implemented in a self-built data transmission system that employs a digital micromirror device to encode OAM channels and realize reference-free calibration simultaneously, thereby enabling a high tolerance to misalignment. We successfully demonstrate high-fidelity transmission of both gray and color images under scattering conditions at an error rate of <0.08%. This technique might open the door to high-performance optical communication in turbulent environments

Encoding of arbitrary micrometric complex illumination patterns with reduced speckle

In nonlinear microscopy, phase-only spatial light modulators (SLMs) allow achieving simultaneous two-photon excitation and fluorescence emission from specific regionof-interests (ROIs). However, as iterative Fourier transform algorithms (IFTAs) can only approximate the illumination of selected ROIs, both image formation and/or signal acquisition can be largely affected by the spatial irregularities of the illumination patterns and the speckle noise. To overcome these limitations, we propose an alternative complex illumination method (CIM) able to generate simultaneous excitation of large-area ROIs with full control over the amplitude and phase of light and reduced speckle. As a proof-of-concept we experimentally demonstrate single-photon and second harmonic generation (SHG) with structured illumination over large-area ROIs

Optical image compression and encryption methods

International audienceOver the years extensive studies have been carried out to apply coherent optics methods in real-time communications and image transmission. This is especially true when a large amount of information needs to be processed, e.g., in high-resolution imaging. The recent progress in data-processing networks and communication systems has considerably increased the capacity of information exchange. However, the transmitted data can be intercepted by nonauthorized people. This explains why considerable effort is being devoted at the current time to data encryption and secure transmission. In addition, only a small part of the overall information is really useful for many applications. Consequently, applications can tolerate information compression that requires important processing when the transmission bit rate is taken into account. To enable efficient and secure information exchange, it is often necessary to reduce the amount of transmitted information. In this context, much work has been undertaken using the principle of coherent optics filtering for selecting relevant information and encrypting it. Compression and encryption operations are often carried out separately, although they are strongly related and can influence each other. Optical processing methodologies, based on filtering, are described that are applicable to transmission and/or data storage. Finally, the advantages and limitations of a set of optical compression and encryption methods are discussed

Source Modulated Multiplexed Hyperspectral Imaging: Theory, Hardware and Application

The design, analysis and application of a multiplexing hyperspectral imager is presented. The hyperspectral imager consists of a broadband digital light projector that uses a digital micromirror array as the optical engine to project light patterns onto a sample object. A single point spectrometer measures light that is reflected from the sample. Multiplexing patterns encode the spectral response from the sample, where each spectrum taken is the sum of a set of spectral responses from a number of pixels. Decoding in software recovers the spectral response of each pixel. A technique, which we call complement encoding, is introduced for the removal of background light effects. Complement encoding requires the use of multiplexing matrices with positive and negative entries. The theory of multiplexing using the Hadamard matrices is developed. Results from prior art are incorporated into a singular notational system under which the different Hadamard matrices are compared with each other and with acquisition of data without multiplexing (pointwise acquisition). The link between Hadamard matrices with strongly regular graphs is extended to incorporate all three types of Hadamard matrices. The effect of the number of measurements used in compressed sensing on measurement precision is derived by inference using results concerning the eigenvalues of large random matrices. The literature shows that more measurements increases accuracy of reconstruction. In contrast we find that more measurement reduces precision, so there is a tradeoff between precision and accuracy. The effect of error in the reference on the Wilcoxon statistic is derived. Reference error reduces the estimate of the Wilcoxon, however given an estimate of theWilcoxon and the proportion of error in the reference, we show thatWilcoxon without error can be estimated. Imaging of simple objects and signal to noise ratio (SNR) experiments are used to test the hyperspectral imager. The simple objects allow us to see that the imager produces sensible spectra. The experiments involve looking at the SNR itself and the SNR boost, that is ratio of the SNR from multiplexing to the SNR from pointwise acquisition. The SNR boost varies dramatically across the spectral domain from 3 to the theoretical maximum of 16. The range of boost values is due to the relative Poisson to additive noise variance changing over the spectral domain, an effect that is due to the light bulb output and detector sensitivity not being flat over the spectral domain. It is shown that the SNR boost is least where the SNR is high and is greatest where the SNR is least, so the boost is provided where it is needed most. The varying SNR boost is interpreted as a preferential boost, that is useful when the dominant noise source is indeterminate or varying. Compressed sensing precision is compared with the accuracy in reconstruction and with the precision in Hadamard multiplexing. A tradeoff is observed between accuracy and precision as the number of measurements increases. Generally Hadamard multiplexing is found to be superior to compressed sensing, but compressed sensing is considered suitable when shortened data acquisition time is important and poorer data quality is acceptable. To further show the use of the hyperspectral imager, volumetric mapping and analysis of beef m. longissimus dorsi are performed. Hyperspectral images are taken of successive slices down the length of the muscle. Classification of the spectra according to visible content as lean or nonlean is trialled, resulting in a Wilcoxon value greater than 0.95, indicating very strong classification power. Analysis of the variation in the spectra down the length of the muscles is performed using variography. The variation in spectra of a muscle is small but increases with distance, and there is a periodic effect possibly due to water seepage from where connective tissue is removed from the meat while cutting from the carcass. The spectra are compared to parameters concerning the rate and value of meat bloom (change of colour post slicing), pH and tenderometry reading (shear force). Mixed results for prediction of blooming parameters are obtained, pH shows strong correlation (R² = 0.797) with the spectral band 598-949 nm despite the narrow range of pH readings obtained. A likewise narrow range of tenderometry readings resulted in no useful correlation with the spectra. Overall the spatial multiplexed imaging with a DMA based light modulation is successful. The theoretical analysis of multiplexing gives a general description of the system performance, particularly for multiplexing with the Hadamard matrices. Experiments show that the Hadamard multiplexing technique improves the SNR of spectra taken over pointwise imaging. Aspects of the theoretical analysis are demonstrated. Hyperspectral images are acquired and analysed that demonstrate that the spectra acquired are sensible and useful