Abstract:
BACKGROUND:Maximum Intensity Projections (MIP) of neuronal dendritic trees obtained from confocal microscopy are frequently used to study the relationship between tree morphology and mechanosensory function in the model organism C. elegans. Extracting dendritic trees from noisy images remains however a strenuous process that has traditionally relied on manual approaches. Here, we focus on automated and reliable 2D segmentations of dendritic trees following a statistical learning framework. METHODS:Our dendritic tree extraction (DTE) method uses small amounts of labelled training data on MIPs to learn noise models of texture-based features from the responses of tree structures and image background. Our strategy lies in evaluating statistical models of noise that account for both the variability generated from the imaging process and from the aggregation of information in the MIP images. These noisy models are then used within a probabilistic, or Bayesian framework to provide a coarse 2D dendritic tree segmentation. Finally, some post-processing is applied to refine the segmentations and provide skeletonized trees using a morphological thinning process. RESULTS:Following a Leave-One-Out Cross Validation (LOOCV) method for an MIP databse with available "ground truth" images, we demonstrate that our approach provides significant improvements in tree-structure segmentations over traditional intensity-based methods. Improvements for MIPs under various imaging conditions are both qualitative and quantitative, as measured from Receiver Operator Characteristic (ROC) curves and the yield and error rates in the final segmentations. In a final step, we demonstrate our DTE approach on previously unseen MIP samples including the extraction of skeletonized structures, and compare our method to a state-of-the art dendritic tree tracing software. CONCLUSIONS:Overall, our DTE method allows for robust dendritic tree segmentations in noisy MIPs, outperforming traditional intensity-based methods. Such approach provides a useable segmentation framework, ultimately delivering a speed-up for dendritic tree identification on the user end and a reliable first step towards further morphological characterizations of tree arborization.
journal_name
Biomed Eng Onlinejournal_title
Biomedical engineering onlineauthors
Greenblum A,Sznitman R,Fua P,Arratia PE,Oren M,Podbilewicz B,Sznitman Jdoi
10.1186/1475-925X-13-74subject
Has Abstractpub_date
2014-06-12 00:00:00pages
74issn
1475-925Xjournal_volume
13pub_type
杂志文章abstract:BACKGROUND:The anterior cruciate ligament (ACL) plays an important role in stabilizing translation and rotation of the tibia relative to the femur. ACL injury alters knee kinematics and usually links to the alternation of gait patterns. The aim of this study is to develop a new method to distinguish between gait patter...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-018-0594-1
更新日期:2018-11-01 00:00:00
abstract:BACKGROUND:In this study, we have examined local non-viral gene delivery, transfection, and therapeutic efficacy of endothelial nitric oxide synthase (eNOS) encoding plasmid DNA administered using coated stents in a rabbit iliac artery restenosis model. METHODS:Lipopolyplexes (LPPs) with eNOS expressing plasmid DNA we...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-9-56
更新日期:2010-09-27 00:00:00
abstract:BACKGROUND:Rotational osteotomy is frequently indicated to correct excessive femoral anteversion in cerebral palsy patients. Angled blade plate is the standard fixation device used when performed in the proximal femur, but extensile exposure is required for plate accommodation. The authors developed a short locked intr...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-10-57
更新日期:2011-06-28 00:00:00
abstract:BACKGROUND:Abnormal blood glucose (BG) concentrations have been associated with increased morbidity and mortality in both critically ill adults and infants. Furthermore, hypoglycaemia and glycaemic variability have both been independently linked to mortality in these patients. Continuous Glucose Monitoring (CGM) device...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-11-45
更新日期:2012-08-06 00:00:00
abstract:BACKGROUND:Entropy analysis has been attracting increasing attentions in the recent two or three decades. It assesses complexity, or irregularity, of time-series which is extraordinarily relevant to physiology and diseases as demonstrated by tremendous studies. However, the complexity can hardly be appreciated by tradi...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-019-0650-5
更新日期:2019-03-20 00:00:00
abstract:BACKGROUND:Electrical impedance tomography (EIT) has been used for functional lung imaging of regional air distributions during mechanical ventilation in intensive care units (ICU). From numerous clinical and animal studies focusing on specific lung functions, a consensus about how to use the EIT technique has been for...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-019-0701-y
更新日期:2019-07-25 00:00:00
abstract:BACKGROUND:Mechanobiological studies allow the characterization of cell response to mechanical stresses. Cells need to be supported by a material with properties similar to the physiological environment. Silicone elastomers have been used to produce various in vitro scaffolds of different geometries for endothelial cel...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-017-0380-5
更新日期:2017-07-14 00:00:00
abstract:BACKGROUND:In stent design optimization, the functional relationship between design parameters and design goals is nonlinear, complex, and implicit and the multi-objective design of stents involves a number of potentially conflicting performance criteria. Therefore it is hard and time-consuming to find the optimal desi...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-016-0268-9
更新日期:2016-12-28 00:00:00
abstract:BACKGROUND:The challenges of glycaemic control in critically ill patients have been debated for 20 years. While glycaemic control shows benefits inter- and intra-patient metabolic variability results in increased hypoglycaemia and glycaemic variability, both increasing morbidity and mortality. Hence, current recommenda...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-019-0720-8
更新日期:2019-10-22 00:00:00
abstract:BACKGROUND:The usability of dexterous hand prostheses is still hampered by the lack of natural and effective control strategies. A decoding strategy based on the processing of descending efferent neural signals recorded using peripheral neural interfaces could be a solution to such limitation. Unfortunately, this choic...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-019-0659-9
更新日期:2019-04-08 00:00:00
abstract:BACKGROUND:Since hemodynamics plays a key role in the development and evolution of cardiovascular pathologies, physician's decision must be based on proper monitoring of relevant physiological flow quantities. METHODS:A numerical analysis of the error introduced by an intravascular Doppler guide wire on the peak veloc...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-016-0234-6
更新日期:2016-10-10 00:00:00
abstract:BACKGROUND:The lumbar range of motion has traditionally been used to assess disability in patients with low back disorders. Controversy exists about how movement ranges in static positions or in a single straight plane is related to the functional status of the patients. The trunk circumduction, as the result of neurom...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-12-4
更新日期:2013-01-11 00:00:00
abstract::The Editors-in-Chief have retracted this article [1] because, after publication, concerns were raised regarding the study design and statistical analysis. Post-publication review has confirmed firstly that within-group changes were highlighted rather than between-group differences as appropriate for a randomized trial...
journal_title:Biomedical engineering online
pub_type: 杂志文章,撤回出版物
doi:10.1186/s12938-020-0749-8
更新日期:2020-01-24 00:00:00
abstract:BACKGROUND:Retina degenerative disorders represent the primary cause of blindness in UK and in the developed world. In particular, Age Related Macular Degeneration (AMD) and Retina Pigmentosa (RP) diseases are of interest to this study. We have therefore created new image processing algorithms for enhancing the visual ...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-9-27
更新日期:2010-06-18 00:00:00
abstract:BACKGROUND:Blood pressure (BP) is associated with early atherosclerosis and plaque rupture because the BP variability can significantly affect the blood flow velocity and shear stress over the plaque. However, the mechanical response of BP variability to the plaque remains unclear. Therefore, we investigated the correl...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-13-152
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:Understanding the mechanical properties of the iris can help to have an insight into the eye diseases with abnormalities of the iris morphology. Material parameters of the iris were simply calculated relying on the ex vivo experiment. However, the mechanical response of the iris in vivo is different from tha...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-13-66
更新日期:2014-05-30 00:00:00
abstract:BACKGROUND:Atherosclerotic plaque progression and rupture are believed to be associated with mechanical stress conditions. In this paper, patient-specific in vivo intravascular ultrasound (IVUS) coronary plaque image data were used to construct computational models with fluid-structure interaction (FSI) and cyclic bend...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-13-32
更新日期:2014-03-26 00:00:00
abstract:BACKGROUND:A valveless pump generates a unidirectional net flow of fluid around a closed loop of soft viscoelastic tubing that is rhythmically compressed at one point. The tubing must have at least two sections with two different stiffnesses. When a short segment of the tube is squeezed asymmetrically at certain freque...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-9-42
更新日期:2010-08-31 00:00:00
abstract:BACKGROUND:It is generally accepted that cartilage adaptation and degeneration are mechanically mediated. Investigating the swelling behaviour of cartilage is important because the stress and strain state of cartilage is associated with the swelling and deformation behaviour. It is well accepted that the swelling of so...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925x-1-8
更新日期:2002-12-19 00:00:00
abstract:BACKGROUND:Computer-assisted arrhythmia recognition is critical for the management of cardiac disorders. Various techniques have been utilized to classify arrhythmias. Generally, these techniques classify two or three arrhythmias or have significantly large processing times. A simpler autoregressive modeling (AR) techn...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925x-1-5
更新日期:2002-11-13 00:00:00
abstract:BACKGROUND:The biomechanical simulation of the human respiratory system is expected to be a useful tool for the diagnosis and treatment of respiratory diseases. Because the deformation of the thorax significantly influences airflow in the lungs, we focused on simulating the thorax deformation by introducing contraction...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-016-0132-y
更新日期:2016-02-06 00:00:00
abstract:BACKGROUND:Biomedical named entity recognition (Bio-NER) is a fundamental task in handling biomedical text terms, such as RNA, protein, cell type, cell line, and DNA. Bio-NER is one of the most elementary and core tasks in biomedical knowledge discovery from texts. The system described here is developed by using the Bi...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-018-0573-6
更新日期:2018-11-06 00:00:00
abstract:BACKGROUND:In a typical electrophysiological experiment, especially one that includes studying animal behavior, the data collected normally contain spikes, local field potentials, behavioral responses and other associated data. In order to obtain informative results, the data must be analyzed simultaneously with the ex...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-017-0419-7
更新日期:2017-11-13 00:00:00
abstract:OBJECTIVE:Heart rate variability (HRV) analysis, which is an important tool for activity assessment of the cardiac autonomic nervous system, very often includes the estimation of power spectra for series of interbeat intervals (IBI). Ectopic beats and artifacts have a destructive effect on the standard methods (Fourier...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-13-138
更新日期:2014-09-23 00:00:00
abstract:BACKGROUND:Since the first well-known electrocardiogram (ECG) delineator based on Wavelet Transform (WT) presented by Li et al. in 1995, a significant research effort has been devoted to the exploitation of this promising method. Its ability to reliably delineate the major waveform components (mono- or bi-phasic P wave...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-10-23
更新日期:2011-04-03 00:00:00
abstract:BACKGROUND:Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal tumors and usually presented with locally advanced and distant metastasis disease, which prevent curative resection or treatments. In this regard, we considered identifying molecular subtypes associated with clinicopathological factor as progn...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-13-S2-S5
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Laser Interstitial ThermoTherapy (LITT) is a well established surgical method. The use of LITT is so far limited to homogeneous tissues, e.g. the liver. One of the reasons is the limited capability of existing treatment planning models to calculate accurately the damage zone. The treatment planning in inhomo...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-4-2
更新日期:2005-01-04 00:00:00
abstract:BACKGROUND:Computational modeling of cardiovascular flow is a growing and useful field, but such simulations usually require the researcher to guess the flow's inlet and outlet conditions since they are difficult and expensive to measure. It is critical to determine the amount of uncertainty introduced by these assumpt...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-018-0497-1
更新日期:2018-05-30 00:00:00
abstract:BACKGROUND:Concerns about the cost-effectiveness of invasive hemodynamic monitoring in critically ill patients using pulmonary artery catheters motivate a renewed search for effective noninvasive methods to measure stroke volume. This paper explores a new approach based on noninvasively measured pulse wave velocity, pu...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/1475-925X-13-137
更新日期:2014-09-19 00:00:00
abstract:BACKGROUND:One of the recommended treatments for disorders associated with the lower extremity venous insufficiency is the application of external mechanical compression. Compression stockings and elastic bandages are widely used for the purpose of compression therapy and are usually designed to exert a specified value...
journal_title:Biomedical engineering online
pub_type: 杂志文章
doi:10.1186/s12938-015-0088-3
更新日期:2015-11-05 00:00:00