scholarly journals Unsupervised Neural Tracing In Densely Labeled Multispectral Brainbow Images

Author(s):  
Bin Duan ◽  
Logan A Walker ◽  
Douglas H Roossien ◽  
Fred Y Shen ◽  
Dawen Cai ◽  
...  
Keyword(s):  
2018 ◽  
Vol 115 (32) ◽  
pp. E7615-E7623 ◽  
Author(s):  
Florencia Garrido-Charad ◽  
Tomas Vega-Zuniga ◽  
Cristián Gutiérrez-Ibáñez ◽  
Pedro Fernandez ◽  
Luciana López-Jury ◽  
...  

The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity.


2018 ◽  
Vol 36 (6) ◽  
pp. 408-414 ◽  
Author(s):  
Jia Wang ◽  
Jingjing Cui ◽  
Chen She ◽  
Dongsheng Xu ◽  
Zhiyun Zhang ◽  
...  

Objectives To compare the neural pathways associated with the tissues located at different traditional acupuncture points in the rat forehead and face using the cholera toxin B subunit (CTB) neural tracing technique. Methods After injection of CTB into the tissues at GB14, ST2 and ST6 in the rat, the neural labelling associated with each acupuncture point was revealed by fluorescent immunohistochemistry of the nervous system, including the trigeminal ganglion (TRG), cervical dorsal root ganglia (DRG), spinal cord and brain. Results The CTB labelling included sensory neurons and their transganglionic axonal terminals, as well as motor neurons. The labelled sensory neurons associated with GB14, ST2 and ST6 were distributed in both the TRG and cervical DRG, and their centrally projected axons terminated in an orderly fashion at their corresponding targets in the spinal trigeminal nucleus and cervical spinal dorsal horn. In addition, labelled motor neurons were observed in the facial motor nucleus, trigeminal motor nucleus and cervical spinal ventral horn, in which facial motor neurons projected to the tissues located at all three acupuncture points. Trigeminal motor neurons innervated both ST2 and ST6, while spinal motor neurons only correlated with ST6. Conclusions These results indicate that the tissues located at each of these three traditional acupuncture points in the rat forehead and face has its own sensory and motor connection with the nervous system in a region-specific pattern through distinct neural pathways. Understanding the neuroanatomical characteristics of acupuncture points from the peripheral nervous system to the central nervous system should help inform acupuncture point selection according to the demands of the clinical situation.


2018 ◽  
Author(s):  
Yan Yan ◽  
Douglas H. Roossien ◽  
Benjamin V. Sadis ◽  
Jason J. Corso ◽  
Dawen Cai

AbstractNeuronal morphology reconstruction in fluorescence microscopy 3D images is essential for analyzing neuronal cell type and connectivity. Manual tracing of neurons in these images is time consuming and subjective. Automated tracing is highly desired yet is one of the foremost challenges in computational neuroscience. The multispectral labeling technique, Brainbow utilizes high dimensional spectral information to distinguish intermingled neuronal processes. It is particular interesting to develop new algorithms to include the spectral information into the tracing process. Recently, deep learning approaches achieved state-of-the-art in different computer vision and medical imaging applications. To benefit from the power of deep learning, in this paper, we propose an automated neural tracing approach in multispectral 3D Brainbow images based on recurrent neural net-work. We first adopt VBM4D approach to denoise multispectral 3D images. Then we generate cubes as training samples along the ground truth, manually traced paths. These cubes are the input to the recur-rent neural network. The proposed approach is simple and effective. The approach can be implemented with the deep learning toolbox ‘Keras’ in 100 lines. Finally, to evaluate our approach, we computed the average and standard deviation of DIADEM metric from the ground truth results to our tracing results, and from our tracing results to the ground truth results. Extensive experimental results on the collected dataset demonstrate that the proposed approach performs well in Brainbow labeled mouse brain images.


2014 ◽  
Vol 306 (5) ◽  
pp. R341-R351 ◽  
Author(s):  
Charles C. Horn ◽  
Kelly Meyers ◽  
Audrey Lim ◽  
Matthew Dye ◽  
Diana Pak ◽  
...  

Signals from the vestibular system, area postrema, and forebrain elicit nausea and vomiting, but gastrointestinal (GI) vagal afferent input arguably plays the most prominent role in defense against food poisoning. It is difficult to determine the contribution of GI vagal afferent input on emesis because various agents (e.g., chemotherapy) often act on multiple sensory pathways. Intragastric copper sulfate (CuSO4) potentially provides a specific vagal emetic stimulus, but its actions are not well defined in musk shrews ( Suncus murinus), a primary small animal model used to study emesis. The aims of the current study were 1) to investigate the effects of subdiaphragmatic vagotomy on CuSO4-induced emesis and 2) to conduct preliminary transneuronal tracing of the GI-brain pathways in musk shrews. Vagotomy failed to inhibit the number of emetic episodes produced by optimal emetic doses of CuSO4 (60 and 120 mg/kg ig), but the effects of lower doses were dependent on an intact vagus (20 and 40 mg/kg). Vagotomy also failed to affect emesis produced by motion (1 Hz, 10 min) or nicotine administration (5 mg/kg sc). Anterograde transport of the H129 strain of herpes simplex virus-1 from the ventral stomach wall identified the following brain regions as receiving inputs from vagal afferents: the nucleus of the solitary tract, area postrema, and lateral parabrachial nucleus. These data indicate that the contribution of vagal pathways to intragastric CuSO4-induced emesis is dose dependent in musk shrews. Furthermore, the current neural tracing data suggest brain stem anatomical circuits that are activated by GI signaling in the musk shrew.


2020 ◽  
Author(s):  
Bin Duan ◽  
Logan A Walker ◽  
Douglas H Roossien ◽  
Fred Y Shen ◽  
Dawen Cai ◽  
...  

AbstractReconstructing neuron morphology is central to uncovering the complexity of the nervous system. That is because the morphology of a neuron essentially provides the physical constraints to its intrinsic electrophysiological properties and its connectivity. Recent advances in imaging technologies generated large quantities of high-resolution 3D images of neurons in the brain. Furthermore, the multispectral labeling technology, Brainbow permits unambiguous differentiation of neighboring neurons in a densely labeled brain, therefore enables for the first time the possibility of studying the connectivity between many neurons from a light microscopy image. However, lack of reliable automated neuron morphology reconstruction makes data analysis the bottleneck of extracting rich informatics in neuroscience. Supervoxel-based neuron segmentation methods have been proposed to solve this problem, however, the use of previous approaches has been impeded by the large numbers of errors which arise in the final segmentation. In this paper, we present a novel unsupervised approach to trace neurons from multispectral Brainbow images, which prevents segmentation errors and tracing continuity errors using two innovations. First, we formulate a Gaussian mixture model-based clustering strategy to improve the separation of segmented color channels that provides accurate skeletonization results for the following steps. Next, a skeleton graph approach is proposed to allow the identification and correction of discontinuities in the neuron tree topology. We find that these innovations allow our approach to outperform current state-of-the-art approaches, which results in more accurate neuron tracing as a tree representation close to human expert annotation.


2021 ◽  
Vol 14 ◽  
Author(s):  
Zhiyun Zhang ◽  
Dongsheng Xu ◽  
Jia Wang ◽  
Jingjing Cui ◽  
Shuang Wu ◽  
...  

Objective: To investigate the sensory and sympathetic innervations associated with both acupoint “Shenshu” (BL23) and kidney in the rat for insight into the neuronal correlation between the Back-Shu Point and its corresponding visceral organ.Methods: The BL23 and kidney were selected as the representative acupoint and visceral organ in this study, in which their local nerve fibers were examined by using double fluorescent immunohistochemistry with calcitonin gene-related peptide (CGRP) and tyrosine hydroxylase (TH). Meanwhile, their neuronal correlation in the dorsal root ganglia (DRGs), spinal cord, and sympathetic (paravertebral) chain were investigated using a double fluorescent neural tracing technique with Alexa Fluor 488 and 594 conjugates with cholera toxin subunit B (AF488/594-CTB).Results: The local tissue of acupoint BL23 and the fibrous capsule of kidney distributed abundantly with CGRP- and TH-positive nerve fibers, corresponding to their sensory and sympathetic innervation. On the other hand, the sensory neurons associated with acupoint BL23 and kidney were labeled with AF488/594-CTB and distributed from thoracic (T) 11 to lumbar (L) 3 DRGs and from T10 to L2 DRGs, respectively, in which some of them in T12-T13 DRGs were simultaneously labeled with both AF488/594-CTB. Also, postganglionic neurons associated with both acupoint BL23 and kidney were found in the sympathetic chain at the same spinal segments but separately labeled with AF488-CTB and AF594-CTB.Conclusion: Our study demonstrates the neural characteristics of the acupoint BL23 and kidney in the rat from the perspective of neurochemistry and neural pathways, providing an example for understanding the neuronal correlation between the Back-Shu Points and their corresponding visceral organs. These results suggest that the stimulation of the Back-Shu Points may regulate the activities of the target-organs via the periphery sensory and sympathetic pathways.


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