Neural organoids have the potential to improve our understanding of human brain development and neurological disorders. However, it remains to be seen whether these tissues can model circuit formation with functional neuronal output. Here, we have adapted air-liquid interface culture to cerebral organoids leading to improved neuronal survival and axon outgrowth. The resulting thick axon tracts display various morphologies including long-range projection within and away from the organoid, growth cone turning, and decussation. Single-cell RNA-sequencing reveals various cortical neuronal identities, and retrograde tracing demonstrates tract morphologies that match proper molecular identities. These cultures exhibit active neuronal networks, and extracortical projecting tracts can innervate mouse spinal cord and evoke contractions of adjacent muscle in a manner dependent on intact organoid-derived innervating tracts. Overall, these results reveal a remarkable self-organization of corticofugal and callosal tracts with a functional output, providing new opportunities to examine relevant aspects of human CNS development and disease.

Dendritic cells (DCs) sample peripheral tissues of the body in search of antigens to present to T cells. This requires two processes, antigen processing and cell motility, originally thought to occur independently. We found that the major histocompatibility complex II-associated invariant chain (Ii or CD74), a known regulator of antigen processing, negatively regulates DC motility in vivo. By using microfabricated channels to mimic the confined environment of peripheral tissues, we found that wild-type DCs alternate between high and low motility, whereas Ii-deficient cells moved in a faster and more uniform manner. The regulation of cell motility by Ii depended on the actin-based motor protein myosin II. Coupling antigen processing and cell motility may enable DCs to more efficiently detect and process antigens within a defined space.

Abstract-A novel adaptive and patch-based approach is proposed for image denoising and representation. The method is based on a pointwise selection of small image patches of fixed size in the variable neighborhood of each pixel. Our contribution is to associate with each pixel the weighted sum of data points within an adaptive neighborhood, in a manner that it balances the accuracy of approximation and the stochastic error, at each spatial position. This method is general and can be applied under the assumption that there exists repetitive patterns in a local neighborhood of a point. By introducing spatial adaptivity, we extend the work earlier described by Buades et al. which can be considered as an extension of bilateral filtering to image patches. Finally, we propose a nearly parameter-free algorithm for image denoising. The method is applied to both artificially corrupted (white Gaussian noise) and real images and the performance is very close to, and in some cases even surpasses, that of the already published denoising methods.

Abstract-We present a non-parametric regression method for denoising 3D image sequences acquired via fluorescence microscopy. The proposed method exploits the redundancy of the 3D+time information to improve the signal-to-noise ratio of images corrupted by PoissonGaussian noise. A variance stabilization transform is first applied to the image-data to remove the dependence between the mean and variance of intensity values. This preprocessing requires the knowledge of parameters related to the acquisition system, also estimated in our approach. In a second step, we propose an original statistical patchbased framework for noise reduction and preservation of space-time discontinuities. In our study, discontinuities are related to small moving spots with high velocity observed in fluorescence video-microscopy. The idea is to minimize an objective non-local energy functional involving spatiotemporal image patches. The minimizer has a simple form and is defined as the weighted average of input data taken in spatially-varying neighborhoods. The size of each neighborhood is optimized to improve the performance of the pointwise estimator. The performance of the algorithm (which requires no motion estimation) is then evaluated on both synthetic and real image sequences using qualitative and quantitative criteria.Index Terms-Video-microscopy, fluorescence, image sequence denoising, patch-based approach, Poisson noise, variance stabilization, adaptive estimation, energy minimization.

Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000× below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.OMX | phototoxicity | image processing | denoising | yeast

A novel adaptive and exemplar-based approach is proposed for image restoration (denoising) and representation. The method is based on a pointwise selection of similar image patches of fixed size in the variable neighborhood of each pixel. The main idea is to associate with each pixel the weighted sum of data points within an adaptive neighborhood. We use small image patches (e.g. 7 × 7 or 9 × 9 patches) to compute these weights since they are able to capture local geometric patterns and texels seen in images. In this paper, we mainly focus on the problem of adaptive neighborhood selection in a manner that balances the accuracy of approximation and the stochastic error, at each spatial position. The proposed pointwise estimator is then iterative and automatically adapts to the degree of underlying smoothness with minimal a priori assumptions on the function to be recovered. The method is applied to artificially corrupted real images and the performance is very close, and in some cases even surpasses, to that of the already published denoising methods. The proposed algorithm is demonstrated on real images corrupted by non-Gaussian noise and is used for applications in bio-imaging.

Partial Differential equations (PDE), wavelets-based methods and neighborhood filters were proposed as locally adaptive machines for noise removal. Recently, Buades, Coll and Morel proposed the Non-Local (NL-) means filter for image denoising. This method replaces a noisy pixel by the weighted average of other image pixels with weights reflecting the similarity between local neighborhoods of the pixel being processed and the other pixels. The NL-means filter was proposed as an intuitive neighborhood filter but theoretical connections to diffusion and non-parametric estimation approaches are also given by the authors. In this paper we propose another bridge, and show that the NL-means filter also emerges from the Bayesian approach with new arguments. Based on this observation, we show how the performance of this filter can be significantly improved by introducing adaptive local dictionaries and a new statistical distance measure to compare patches. The new Bayesian NL-means filter is better parametrized and the amount of smoothing is directly determined by the noise variance (estimated from image data) given the patch size. Experimental results are given for real images with artificial Gaussian noise added, and for images with real imagedependent noise.

Localization of single molecules in microscopy images is a key step in quantitative single particle data analysis. Among them, single molecule based super-resolution optical microscopy techniques require high localization accuracy as well as computation of large data sets in the order of 10(5) single molecule detections to reconstruct a single image. We hereby present an algorithm based on image wavelet segmentation and single particle centroid determination, and compare its performance with the commonly used gaussian fitting of the point spread function. We performed realistic simulations at different signal-to-noise ratios and particle densities and show that the calculation time using the wavelet approach can be more than one order of magnitude faster than that of gaussian fitting without a significant degradation of the localization accuracy, from 1 nm to 4 nm in our range of study. We propose a simulation-based estimate of the resolution of an experimental single molecule acquisition.