Optimization of Traced Neuron Skeleton Using Lasso-Based Model

Reconstruction of neuronal morphology from images involves mainly the extraction of neuronal skeleton points. It is an indispensable step in the quantitative analysis of neurons. Due to the complex morphology of neurons, many widely used tracing methods have difficulties in accurately acquiring skeleton points near branch points or in structures with tortuosity. Here, we propose two models to solve these problems. One is based on an L1-norm minimization model, which can better identify tortuous structure, namely, a local structure with large curvature skeleton points; the other detects an optimized branch point by considering the combination patterns of all neurites that link to this point. We combined these two models to achieve optimized skeleton detection for a neuron. We validate our models in various datasets including MOST and BigNeuron. In addition, we demonstrate that our method can optimize the traced skeletons from large-scale images. These characteristics of our approach indicate that it can reduce manual editing of traced skeletons and help to accelerate the accurate reconstruction of neuronal morphology

DeepBouton: Automated Identification of Single-Neuron Axonal Boutons at the Brain-Wide Scale

Fine morphological reconstruction of individual neurons across the entire brain is essential for mapping brain circuits. Inference of presynaptic axonal boutons, as a key part of single-neuron fine reconstruction, is critical for interpreting the patterns of neural circuit wiring schemes. However, automated bouton identification remains challenging for current neuron reconstruction tools, as they focus mainly on neurite skeleton drawing and have difficulties accurately quantifying bouton morphology. Here, we developed an automated method for recognizing single-neuron axonal boutons in whole-brain fluorescence microscopy datasets. The method is based on deep convolutional neural networks and density-peak clustering. High-dimensional feature representations of bouton morphology can be learned adaptively through convolutional networks and used for bouton recognition and subtype classification. We demonstrate that the approach is effective for detecting single-neuron boutons at the brain-wide scale for both long-range pyramidal projection neurons and local interneurons

Additional file 1: of Large-scale localization of touching somas from 3D images using density-peak clustering

Detailed derivation of the proposed method complexity. (PDF 104 kb

ParamNet: A Parameter-variable Network for Fast Stain Normalization

In practice, digital pathology images are often affected by various factors, resulting in very large differences in color and brightness. Stain normalization can effectively reduce the differences in color and brightness of digital pathology images, thus improving the performance of computer-aided diagnostic systems. Conventional stain normalization methods rely on one or several reference images, but one or several images are difficult to represent the entire dataset. Although learning-based stain normalization methods are a general approach, they use complex deep networks, which not only greatly reduce computational efficiency, but also risk introducing artifacts. StainNet is a fast and robust stain normalization network, but it has not a sufficient capability for complex stain normalization due to its too simple network structure. In this study, we proposed a parameter-variable stain normalization network, ParamNet. ParamNet contains a parameter prediction sub-network and a color mapping sub-network, where the parameter prediction sub-network can automatically determine the appropriate parameters for the color mapping sub-network according to each input image. The feature of parameter variable ensures that our network has a sufficient capability for various stain normalization tasks. The color mapping sub-network is a fully 1x1 convolutional network with a total of 59 variable parameters, which allows our network to be extremely computationally efficient and does not introduce artifacts. The results on cytopathology and histopathology datasets show that our ParamNet outperforms state-of-the-art methods and can effectively improve the generalization of classifiers on pathology diagnosis tasks. The code has been available at https://github.com/khtao/ParamNet