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Background Automated detection and segmentation of somas in fluorescent images of neurons is a major goal in quantitative studies of neuronal networks, including applications of high-content-screenings where it is required to quantify multiple morphological properties of neurons. Despite recent advances in image processing targeted to neurobiological applications, existing algorithms of soma detection are often unreliable, especially when processing fluorescence image stacks of neuronal cultures. New method In this paper, we introduce an innovative algorithm for the detection and extraction of somas in fluorescent images of networks of cultured neurons where somas and other structures exist in the same fluorescent channel. Our method relies on a new geometrical descriptor called Directional Ratio and a collection of multiscale orientable filters to quantify the level of local isotropy in an image. To optimize the application of this approach, we introduce a new construction of multiscale anisotropic filters that is implemented by separable convolution. Results Extensive numerical experiments using 2D and 3D confocal images show that our automated algorithm reliably detects somas, accurately segments them, and separates contiguous ones. Comparison with existing methods We include a detailed comparison with state-of-the-art existing methods to demonstrate that our algorithm is extremely competitive in terms of accuracy, reliability and computational efficiency. Conclusions Our algorithm will facilitate the development of automated platforms for high content neuron image processing. A Matlab code is released open-source and freely available to the scientific community. [ABSTRACT FROM AUTHOR]

We propose a shearlet formulation of the total variation (TV) method for denoising images. Shearlets have been mathematically proven to represent distributed discontinuities such as edges better than traditional wavelets and are a suitable tool for edge characterization. Common approaches in combining wavelet-like representations such as curvelets with TV or diffusion methods aim at reducing Gibbs-type artifacts after obtaining a nearly optimal estimate. We show that it is possible to obtain much better estimates from a shearlet representation by constraining the residual coefficients using a projected adaptive total variation scheme in the shearlet domain. We also analyze the performance of a shearlet-based diffusion method. Numerical examples demonstrate that these schemes are highly effective at denoising complex images and outperform a related method based on the use of the curvelet transform. Furthermore, the shearlet-TV scheme requires far fewer iterations than similar competitors. [ABSTRACT FROM AUTHOR]