Abstract:
:Recent studies have supported the relation between mitochondrial functions and degenerative disorders related to ageing, such as Alzheimer's and Parkinson's diseases. Since these studies have exposed the need for detailed and high-resolution analysis of physical alterations in mitochondria, it is necessary to be able to perform segmentation and 3D reconstruction of mitochondria. However, due to the variety of mitochondrial structures, automated mitochondria segmentation and reconstruction in electron microscopy (EM) images have proven to be a difficult and challenging task. This paper puts forward an effective and automated pipeline based on deep learning to realize mitochondria segmentation in different EM images. The proposed pipeline consists of three parts: (1) utilizing image registration and histogram equalization as image pre-processing steps to maintain the consistency of the dataset; (2) proposing an effective approach for 3D mitochondria segmentation based on a volumetric, residual convolutional and deeply supervised network; and (3) employing a 3D connection method to obtain the relationship of mitochondria and displaying the 3D reconstruction results. To our knowledge, we are the first researchers to utilize a 3D fully residual convolutional network with a deeply supervised strategy to improve the accuracy of mitochondria segmentation. The experimental results on anisotropic and isotropic EM volumes demonstrate the effectiveness of our method, and the Jaccard index of our segmentation (91.8% in anisotropy, 90.0% in isotropy) and F1 score of detection (92.2% in anisotropy, 90.9% in isotropy) suggest that our approach achieved state-of-the-art results. Our fully automated pipeline contributes to the development of neuroscience by providing neurologists with a rapid approach for obtaining rich mitochondria statistics and helping them elucidate the mechanism and function of mitochondria.
journal_name
Front Neuroanatjournal_title
Frontiers in neuroanatomyauthors
Xiao C,Chen X,Li W,Li L,Wang L,Xie Q,Han Hdoi
10.3389/fnana.2018.00092subject
Has Abstractpub_date
2018-11-02 00:00:00pages
92issn
1662-5129journal_volume
12pub_type
杂志文章abstract::Rafael Lorente de Nó, the youngest of Santiago Ramón y Cajal disciples, was one of the last Century's more influential researches in neuroscience. This assay highlights two fundamental contributions of Rafael Lorente de Nó to neurobiology: the intrinsic organization of the mammalian cerebral cortex and the basic physi...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2014.00147
更新日期:2014-12-03 00:00:00
abstract::Sevoflurane is widely used in adult and pediatric patients during clinical surgeries. Although studies have shown that exposure to sevoflurane impairs solfactory memory after an operation, the neuropathological changes underlying this effect are not clear. This study detected the effect of sevoflurane exposure on the ...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2016.00072
更新日期:2016-06-24 00:00:00
abstract::Brain tissue contains autofluorescing elements that potentially impede accurate identification of neurons when visualized with fluorescent microscopy. Age-related accumulation of molecules with autofluorescent properties, such as lipofuscin, can possess spectral profiles that invade the typical emission range of fluor...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2019.00073
更新日期:2019-07-18 00:00:00
abstract::Embryonic development in mammals has evolved a platform for genomic conflict between mothers and embryos and, by extension, between maternal and paternal genomes. The evolutionary interests of the mother and embryo may be maximized through the promotion of sex-chromosome genes and imprinted alleles, resulting in the r...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2013.00002
更新日期:2013-04-09 00:00:00
abstract::Cortical networks are shaped by sensory experience and are most susceptible to modifications during critical periods characterized by enhanced plasticity at the structural and functional level. A system particularly well-studied in this context is the mammalian visual system. Plasticity has been documented for the som...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2014.00011
更新日期:2014-03-11 00:00:00
abstract::Biological impacts of light beyond vision, i.e., non-visual functions of light, signify the need to better understand light detection (or photoreception) systems in vertebrates. Photopigments, which comprise light-absorbing chromophores bound to a variety of G-protein coupled receptor opsins, are responsible for visua...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2016.00048
更新日期:2016-04-27 00:00:00
abstract::Gaze changes involving the eyes and head are orchestrated by brainstem gaze centers found within the superior colliculus (SC), paramedian pontine reticular formation (PPRF), and medullary reticular formation (MdRF). The mesencephalic reticular formation (MRF) also plays a role in gaze. It receives a major input from t...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2013.00055
更新日期:2014-01-10 00:00:00
abstract::Dendrite and dendritic spine formation are crucial for proper brain function. DISC1-binding zinc finger protein (DBZ) was first identified as a Disrupted-In-Schizophrenia1 (DISC1) binding partner. DBZ is highly expressed in the cerebral cortex of developing and adult rodents and is involved in neurite formation, cell ...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2015.00052
更新日期:2015-04-30 00:00:00
abstract::We evaluated the neuropil distribution of the enzymes NADPH diaphorase (NADPH-d) and cytochrome oxidase (CO) in the spinal cord of the agouti, a medium-sized diurnal rodent, together with the distribution pattern and morphometrical characteristics of NADPH-d reactive neurons across different spinal segments. Neuropil ...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/neuro.05.002.2008
更新日期:2008-05-26 00:00:00
abstract::Experimentalallergic encephalomyelitis (EAE) is an animal model for inflammatory demyelinating autoimmune disease, i.e., multiple sclerosis (MS). In the present study, we investigated the antineuroinflammatory/neuroprotective effects of C16, an ανβ3 integrin-binding peptide, and recombinant rat ciliary neurotrophic fa...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2013.00044
更新日期:2013-12-30 00:00:00
abstract::Cortical calretinin (CR)-expressing interneurons represent a heterogeneous subpopulation of about 10-30% of GABAergic interneurons, which altogether total ca. 12-20% of all cortical neurons. In the rodent neocortex, CR cells display different somatodendritic morphologies ranging from bipolar to multipolar but the bipo...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2014.00052
更新日期:2014-06-24 00:00:00
abstract::Most studies in mammals and birds have demonstrated common patterns of hypothalamic development highlighted by the combination of developmental regulatory genes (genoarchitecture), supporting the notion of the hypothalamus as a component of the secondary prosencephalon, topologically rostral to the diencephalon. In ou...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2015.00003
更新日期:2015-02-03 00:00:00
abstract::Early telencephalic development involves the migration of diverse cell types that can be identified by specific molecular markers. Most prominent among them are Cajal-Retzius (CR) cells that emanate mainly from the cortical hem and to a lesser extent from rostrolateral, septal and caudo-medial regions. One additional ...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2017.00097
更新日期:2017-11-01 00:00:00
abstract::Really interesting new gene (RING) finger protein is a type of zinc-binding motif found in a large family of functionally distinct proteins. RING finger proteins are involved in diverse cellular processes including apoptosis, DNA repair, cell cycle, signal transduction, tumour suppressor, vesicular transport, and pero...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2017.00072
更新日期:2017-08-31 00:00:00
abstract::[This corrects the article on p. 99 in vol. 9, PMID: 26300740.]. ...
journal_title:Frontiers in neuroanatomy
pub_type: 已发布勘误
doi:10.3389/fnana.2015.00146
更新日期:2015-11-17 00:00:00
abstract::Over the last 60 years, the spotlight of research has periodically returned to the cerebellum as new techniques and insights have emerged. Because of its simple homogeneous structure, limited diversity of cell types and characteristic behavioral pathologies, the cerebellum is a natural home for studies of cell specifi...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2013.00029
更新日期:2013-09-03 00:00:00
abstract::The study of the links and interactions between development and motor learning has noticeable implications for the understanding and management of neurodevelopmental disorders. This is particularly relevant for the cerebellum which is critical for sensorimotor learning. The olivocerebellar pathway is a key pathway con...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2012.00001
更新日期:2012-01-23 00:00:00
abstract::Gestational exposure to valproic acid (VPA) is known to cause behavioral deficits of sociability, matching similar alterations in human autism spectrum disorder (ASD). Available data are scarce on the neuromorphological changes in VPA-exposed animals. Here, we focused on alterations of the dopaminergic system, which i...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2020.00029
更新日期:2020-06-05 00:00:00
abstract::Calcium stores in neurons are heterogeneous in compartmentalization and molecular composition. Danio rerio (zebrafish) is an animal model with a simply folded cerebellum similar in cellular organization to that of mammals. The aim of the study was to identify new endoplasmic reticulum (ER) calcium store markers in zeb...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2020.00015
更新日期:2020-04-21 00:00:00
abstract::Emotions depend upon the integrated activity of neural networks that modulate arousal, autonomic function, motor control, and somatosensation. Brainstem nodes play critical roles in each of these networks, but prior studies of the neuroanatomic basis of emotion, particularly in the human neuropsychological literature,...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2017.00015
更新日期:2017-03-09 00:00:00
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journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2020.00010
更新日期:2020-03-18 00:00:00
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journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2017.00106
更新日期:2017-11-24 00:00:00
abstract::Gaucher's disease (GD) is the most prevalent lysosomal storage disorder. GD is caused by homozygous mutations of the GBA1 gene, which codes for beta-glucocerebrosidase (GCase). Although GD primarily affects peripheral tissues, the presence of neurological symptoms has been reported in several GD subtypes. GBA1 mutatio...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2018.00052
更新日期:2018-06-28 00:00:00
abstract::Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here,...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2015.00069
更新日期:2015-06-04 00:00:00
abstract::Although the olfactory sense has always been considered with less interest than the visual, auditive or somatic senses, it does plays a major role in our ordinary life, with important implication in dangerous situations or in social and emotional behaviors. Traditional Diffusion Tensor signal model and related tractog...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2017.00032
更新日期:2017-04-10 00:00:00
abstract::A key challenge in cortical neuroscience is to gain a comprehensive understanding of how pyramidal neuron heterogeneity across different areas and species underlies the functional specialization of individual neurons, networks, and areas. Comparative studies have been important in this endeavor, providing data relevan...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章,评审
doi:10.3389/fnana.2017.00011
更新日期:2017-03-07 00:00:00
abstract::The development of the mammalian neocortex relies heavily on subplate. The proportion of this cell population varies considerably in different mammalian species. Subplate is almost undetectable in marsupials, forms a thin, but distinct layer in mouse and rat, a larger layer in carnivores and big-brained mammals as pig...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2011.00025
更新日期:2011-04-07 00:00:00
abstract::How does the size of the glial and neuronal cells that compose brain tissue vary across brain structures and species? Our previous studies indicate that average neuronal size is highly variable, while average glial cell size is more constant. Measuring whole cell sizes in vivo, however, is a daunting task. Here we use...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2014.00127
更新日期:2014-11-12 00:00:00
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journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2013.00018
更新日期:2013-06-26 00:00:00
abstract::Striatal dopamine (DA) denervation results in a significant loss of dendritic spines on medium spiny projection neurons in Parkinson's disease. In 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated parkinsonian monkeys, spines contacted either by cortical or thalamic glutamatergic terminals are severely affected on ...
journal_title:Frontiers in neuroanatomy
pub_type: 杂志文章
doi:10.3389/fnana.2010.00133
更新日期:2010-12-10 00:00:00