A Multiscale Ray-Shooting Model for Termination Detection of Tree-Like Structures in Biomedical Images

Tracing weak neuron fibers

MOTIVATION

Precise reconstruction of neuronal arbors is important for circuitry mapping. Many auto-tracing algorithms have been developed toward full reconstruction. However, it is still challenging to trace the weak signals of neurite fibers that often correspond to axons.

RESULTS

We proposed a method, named the NeuMiner, for tracing weak fibers by combining two strategies: an online sample mining strategy and a modified gamma transformation. NeuMiner improved the recall of weak signals (voxel values <20) by a large margin, from 5.1 to 27.8%. This is prominent for axons, which increased by 6.4 times, compared to 2.0 times for dendrites. Both strategies were shown to be beneficial for weak fiber recognition, and they reduced the average axonal spatial distances to gold standards by 46 and 13%, respectively. The improvement was observed on two prevalent automatic tracing algorithms and can be applied to any other tracers and image types.

AVAILABILITY AND IMPLEMENTATION

Source codes of NeuMiner are freely available on GitHub (https://github.com/crazylyf/neuronet/tree/semantic_fnm). Image visualization, preprocessing and tracing are conducted on the Vaa3D platform, which is accessible at the Vaa3D GitHub repository (https://github.com/Vaa3D). All training and testing images are cropped from high-resolution fMOST mouse brains downloaded from the Brain Image Library (https://www.brainimagelibrary.org/), and the corresponding gold standards are available at https://doi.brainimagelibrary.org/doi/10.35077/g.25.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Deep-Learning-Based Automated Neuron Reconstruction From 3D Microscopy Images Using Synthetic Training Images

Digital reconstruction of neuronal structures from 3D microscopy images is critical for the quantitative investigation of brain circuits and functions. It is a challenging task that would greatly benefit from automatic neuron reconstruction methods. In this paper, we propose a novel method called SPE-DNR that combines spherical-patches extraction (SPE) and deep-learning for neuron reconstruction (DNR). Based on 2D Convolutional Neural Networks (CNNs) and the intensity distribution features extracted by SPE, it determines the tracing directions and classifies voxels into foreground or background. This way, starting from a set of seed points, it automatically traces the neurite centerlines and determines when to stop tracing. To avoid errors caused by imperfect manual reconstructions, we develop an image synthesizing scheme to generate synthetic training images with exact reconstructions. This scheme simulates 3D microscopy imaging conditions as well as structural defects, such as gaps and abrupt radii changes, to improve the visual realism of the synthetic images. To demonstrate the applicability and generalizability of SPE-DNR, we test it on 67 real 3D neuron microscopy images from three datasets. The experimental results show that the proposed SPE-DNR method is robust and competitive compared with other state-of-the-art neuron reconstruction methods.

Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains

Recent advances in brain imaging allow producing large amounts of 3-D volumetric data from which morphometry data is reconstructed and measured. Fine detailed structural morphometry of individual neurons, including somata, dendrites, axons, and synaptic connectivity based on digitally reconstructed neurons, is essential for cataloging neuron types and their connectivity. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of 1,050 neurons including their dendrites and full axons, and detected 1.9 million putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.

Deep Reinforcement Learning-Based Progressive Sequence Saliency Discovery Network for Mitosis Detection In Time-Lapse Phase-Contrast Microscopy Images

Mitosis detection plays an important role in the analysis of cell status and behavior and is therefore widely utilized in many biological research and medical applications. In this article, we propose a deep reinforcement learning-based progressive sequence saliency discovery network (PSSD)for mitosis detection in time-lapse phase contrast microscopy images. By discovering the salient frames when cell state changes in the sequence, PSSD can more effectively model the mitosis process for mitosis detection. We formulate the discovery of salient frames as a Markov Decision Process (MDP)that progressively adjusts the selection positions of salient frames in the sequence, and further leverage deep reinforcement learning to learn the policy in the salient frame discovery process. The proposed method consists of two parts: 1)the saliency discovery module that selects the salient frames from the input cell image sequence by progressively adjusting the selection positions of salient frames; 2)the mitosis identification module that takes a sequence of salient frames and performs temporal information fusion for mitotic sequence classification. Since the policy network of the saliency discovery module is trained under the guidance of the mitosis identification module, PSSD can comprehensively explore the salient frames that are beneficial for mitosis detection. To our knowledge, this is the first work to implement deep reinforcement learning to the mitosis detection problem. In the experiment, we evaluate the proposed method on the largest mitosis detection dataset, C2C12-16. Experiment results show that compared with the state-of-the-arts, the proposed method can achieve significant improvement for both mitosis identification and temporal localization on C2C12-16.

An O-shape Neural Network With Attention Modules to Detect Junctions in Biomedical Images Without Segmentation

Junction plays an important role in biomedical research such as retinal biometric identification, retinal image registration, eye-related disease diagnosis and neuron reconstruction. However, junction detection in original biomedical images is extremely challenging. For example, retinal images contain many tiny blood vessels with complicated structures and low contrast, which makes it challenging to detect junctions. In this paper, we propose an O-shape Network architecture with Attention modules (Attention O-Net), which includes Junction Detection Branch (JDB) and Local Enhancement Branch (LEB) to detect junctions in biomedical images without segmentation. In JDB, the heatmap indicating the probabilities of junctions is estimated and followed by choosing the positions with the local highest value as the junctions, whereas it is challenging to detect junctions when the images contain weak filament signals. Therefore, LEB is constructed to enhance the thin branch foreground and make the network pay more attention to the regions with low contrast, which is helpful to alleviate the imbalance of the foreground between thin and thick branches and to detect the junctions of the thin branch. Furthermore, attention modules are utilized to introduce the feature maps from LEB to JDB, which can establish a complementary relationship and further integrate local features and contextual information between the two branches. The proposed method achieves the highest average F1-scores of 0.82, 0.73 and 0.94 in two retinal datasets and one neuron dataset, respectively. The experimental results confirm that Attention O-Net outperforms other state-of-the-art detection methods, and is helpful for retinal biometric identification.

Efficient 3D Junction Detection in Biomedical Images Based on a Circular Sampling Model and Reverse Mapping

Detection and localization of terminations and junctions is a key step in the morphological reconstruction of tree-like structures in images. Previously, a ray-shooting model was proposed to detect termination points automatically. In this paper, we propose an automatic method for 3D junction points detection in biomedical images, relying on a circular sampling model and a 2D-to-3D reverse mapping approach. First, the existing ray-shooting model is improved to a circular sampling model to extract the pixel intensity distribution feature across the potential branches around the point of interest. The computation cost can be reduced dramatically compared to the existing ray-shooting model. Then, the Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm is employed to detect 2D junction points in maximum intensity projections (MIPs) of sub-volume images in a given 3D image, by determining the number of branches in the candidate junction region. Further, a 2D-to-3D reverse mapping approach is used to map these detected 2D junction points in MIPs to the 3D junction points in the original 3D images. The proposed 3D junction point detection method is implemented as a build-in tool in the Vaa3D platform. Experiments on multiple 2D images and 3D images show average precision and recall rates of 87.11% and 88.33% respectively. In addition, the proposed algorithm is dozens of times faster than the existing deep-learning based model. The proposed method has excellent performance in both detection precision and computation efficiency for junction detection even in large-scale biomedical images.

Neuron Image Segmentation via Learning Deep Features and Enhancing Weak Neuronal Structures

Neuron morphology reconstruction (tracing) in 3D volumetric images is critical for neuronal research. However, most existing neuron tracing methods are not applicable in challenging datasets where the neuron images are contaminated by noises or containing weak filament signals. In this paper, we present a two-stage 3D neuron segmentation approach via learning deep features and enhancing weak neuronal structures, to reduce the impact of image noise in the data and enhance the weak-signal neuronal structures. In the first stage, we train a voxel-wise multi-level fully convolutional network (FCN), which specializes in learning deep features, to obtain the 3D neuron image segmentation maps in an end-to-end manner. In the second stage, a ray-shooting model is employed to detect the discontinued segments in segmentation results of the first-stage, and the local neuron diameter of the broken point is estimated and direction of the filamentary fragment is detected by rayburst sampling algorithm. Then, a Hessian-repair model is built to repair the broken structures, by enhancing weak neuronal structures in a fibrous structure determined by the estimated local neuron diameter and the filamentary fragment direction. Experimental results demonstrate that our proposed segmentation approach achieves better segmentation performance than other state-of-the-art methods for 3D neuron segmentation. Compared with the neuron reconstruction results on the segmented images produced by other segmentation methods, the proposed approach gains 47.83% and 34.83% improvement in the average distance scores. The average Precision and Recall rates of the branch point detection with our proposed method are 38.74% and 22.53% higher than the detection results without segmentation.

Spherical-Patches Extraction for Deep-Learning-Based Critical Points Detection in 3D Neuron Microscopy Images

Digital reconstruction of neuronal structures is very important to neuroscience research. Many existing reconstruction algorithms require a set of good seed points. 3D neuron critical points, including terminations, branch points and cross-over points, are good candidates for such seed points. However, a method that can simultaneously detect all types of critical points has barely been explored. In this work, we present a method to simultaneously detect all 3 types of 3D critical points in neuron microscopy images, based on a spherical-patches extraction (SPE) method and a 2D multi-stream convolutional neural network (CNN). SPE uses a set of concentric spherical surfaces centered at a given critical point candidate to extract intensity distribution features around the point. Then, a group of 2D spherical patches is generated by projecting the surfaces into 2D rectangular image patches according to the orders of the azimuth and the polar angles. Finally, a 2D multi-stream CNN, in which each stream receives one spherical patch as input, is designed to learn the intensity distribution features from those spherical patches and classify the given critical point candidate into one of four classes: termination, branch point, cross-over point or non-critical point. Experimental results confirm that the proposed method outperforms other state-of-the-art critical points detection methods. The critical points based neuron reconstruction results demonstrate the potential of the detected neuron critical points to be good seed points for neuron reconstruction. Additionally, we have established a public dataset dedicated for neuron critical points detection, which has been released along with this article.

3D Neuron Microscopy Image Segmentation via the Ray-Shooting Model and a DC-BLSTM Network

The morphology reconstruction (tracing) of neurons in 3D microscopy images is important to neuroscience research. However, this task remains very challenging because of the low signal-to-noise ratio (SNR) and the discontinued segments of neurite patterns in the images. In this paper, we present a neuronal structure segmentation method based on the ray-shooting model and the Long Short-Term Memory (LSTM)-based network to enhance the weak-signal neuronal structures and remove background noise in 3D neuron microscopy images. Specifically, the ray-shooting model is used to extract the intensity distribution features within a local region of the image. And we design a neural network based on the dual channel bidirectional LSTM (DC-BLSTM) to detect the foreground voxels according to the voxel-intensity features and boundary-response features extracted by multiple ray-shooting models that are generated in the whole image. This way, we transform the 3D image segmentation task into multiple 1D ray/sequence segmentation tasks, which makes it much easier to label the training samples than many existing Convolutional Neural Network (CNN) based 3D neuron image segmentation methods. In the experiments, we evaluate the performance of our method on the challenging 3D neuron images from two datasets, the BigNeuron dataset and the Whole Mouse Brain Sub-image (WMBS) dataset. Compared with the neuron tracing results on the segmented images produced by other state-of-the-art neuron segmentation methods, our method improves the distance scores by about 32% and 27% in the BigNeuron dataset, and about 38% and 27% in the WMBS dataset.

Neuronal Population Reconstruction From Ultra-Scale Optical Microscopy Images via Progressive Learning

Reconstruction of neuronal populations from ultra-scale optical microscopy (OM) images is essential to investigate neuronal circuits and brain mechanisms. The noises, low contrast, huge memory requirement, and high computational cost pose significant challenges in the neuronal population reconstruction. Recently, many studies have been conducted to extract neuron signals using deep neural networks (DNNs). However, training such DNNs usually relies on a huge amount of voxel-wise annotations in OM images, which are expensive in terms of both finance and labor. In this paper, we propose a novel framework for dense neuronal population reconstruction from ultra-scale images. To solve the problem of high cost in obtaining manual annotations for training DNNs, we propose a progressive learning scheme for neuronal population reconstruction (PLNPR) which does not require any manual annotations. Our PLNPR scheme consists of a traditional neuron tracing module and a deep segmentation network that mutually complement and progressively promote each other. To reconstruct dense neuronal populations from a terabyte-sized ultra-scale image, we introduce an automatic framework which adaptively traces neurons block by block and fuses fragmented neurites in overlapped regions continuously and smoothly. We build a dataset "VISoR-40" which consists of 40 large-scale OM image blocks from cortical regions of a mouse. Extensive experimental results on our VISoR-40 dataset and the public BigNeuron dataset demonstrate the effectiveness and superiority of our method on neuronal population reconstruction and single neuron reconstruction. Furthermore, we successfully apply our method to reconstruct dense neuronal populations from an ultra-scale mouse brain slice. The proposed adaptive block propagation and fusion strategies greatly improve the completeness of neurites in dense neuronal population reconstruction.

DeepBranch: Deep Neural Networks for Branch Point Detection in Biomedical Images

Morphology reconstruction of tree-like structures in volumetric images, such as neurons, retinal blood vessels, and bronchi, is of fundamental interest for biomedical research. 3D branch points play an important role in many reconstruction applications, especially for graph-based or seed-based reconstruction methods and can help to visualize the morphology structures. There are a few hand-crafted models proposed to detect the branch points. However, they are highly dependent on the empirical setting of the parameters for different images. In this paper, we propose a DeepBranch model for branch point detection with two-level designed convolutional networks, a candidate region segmenter and a false positive reducer. On the first level, an improved 3D U-Net model with anisotropic convolution kernels is employed to detect initial candidates. Compared with the traditional sliding window strategy, the improved 3D U-Net can avoid massive redundant computations and dramatically speed up the detection process by employing dense-inference with fully convolutional neural networks (FCN). On the second level, a method based on multi-scale multi-view convolutional neural networks (MSMV-Net) is proposed for false positive reduction by feeding multi-scale views of 3D volumes into multiple streams of 2D convolution neural networks (CNNs), which can take full advantage of spatial contextual information as well as fit different sizes. Experiments on multiple 3D biomedical images of neurons, retinal blood vessels and bronchi confirm that the proposed 3D branch point detection method outperforms other state-of-the-art detection methods, and is helpful for graph-based or seed-based reconstruction methods.