Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Nature Methods, Journal Year: 2024, Volume and Issue: 21(5), P. 804 - 808

Published: Jan. 8, 2024

Language: Английский

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The importance of 3D fibre architecture in cancer and implications for biomaterial model design

Nature reviews. Cancer, Journal Year: 2024, Volume and Issue: 24(7), P. 461 - 479

Published: June 17, 2024

Language: Английский

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Retinal image blood vessel classification using hybrid deep learning in cataract diseased fundus images

Biomedical Signal Processing and Control, Journal Year: 2023, Volume and Issue: 84, P. 104776 - 104776

Published: March 10, 2023

Language: Английский

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Microphysiological model of PIK3CA-driven vascular malformations reveals a role of dysregulated Rac1 and mTORC1/2 in lesion formation

Science Advances, Journal Year: 2023, Volume and Issue: 9(7)

Published: Feb. 15, 2023

Somatic activating mutations of

Language: Английский

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Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs

Cell Reports Methods, Journal Year: 2023, Volume and Issue: 3(3), P. 100436 - 100436

Published: March 1, 2023

Light-sheet fluorescence microscopy (LSFM) can produce high-resolution tomograms of tissue vasculature with high accuracy. However, data processing and analysis is laborious due to the size datasets. Here, we introduce VesselExpress, an automated software that reliably analyzes six characteristic vascular network parameters including vessel diameter in LSFM on average computing hardware. VesselExpress ∼100 times faster than other existing tools, requires no user interaction, integrates batch parallelization. Employing innovative dual Frangi filter approach, show obesity induces a large-scale modulation brain mice seven major organs differ strongly their 3D makeup. Hence, transforms from observational analytical working tool.

Language: Английский

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Reconstructing microvascular network skeletons from 3D images: What is the ground truth?

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 171, P. 108140 - 108140

Published: Feb. 27, 2024

Structural changes to microvascular networks are increasingly highlighted as markers of pathogenesis in a wide range disease, e.g. Alzheimer's vascular dementia and tumour growth. This has motivated the development dedicated 3D imaging techniques, alongside creation computational modelling frameworks capable using reconstructed simulate functional behaviours such blood flow or transport processes. Extraction from data broadly consists two image processing steps: segmentation followed by skeletonisation. Much research effort been devoted field, there standard widely-applied methodologies for creating assessing gold standards ground truths produced manual annotation automated algorithms. The Skeletonisation however, lacks widely applied, simple compute metrics validation optimisation numerous algorithms that exist extract skeletons binary images. is particularly problematic datasets increase size visual inspection becomes an insufficient approach. In this work, we first demonstrate extent problem applying 4 widely-used skeletonisation 3 different datasets. doing so show significant variability between same segmented dataset. Moreover, structural propagates simulated flow. To mitigate introduce new, fast easy super metric compares volume, connectivity, medialness, bifurcation point identification homology original data. We then can be used select best performing algorithm given dataset, well optimize its parameters. Finally, also quickly identify how particular could improved, becoming powerful tool understanding complex implication small network.

Language: Английский

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Large Scale in vivo Acquisition, Segmentation and 3D Reconstruction of Cortical Vasculature using $$\mu $$Doppler Ultrasound Imaging

Neuroinformatics, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 14, 2025

The brain is composed of a dense and ramified vascular network arteries, veins capillaries various sizes. One way to assess the risk cerebrovascular pathologies use computational models predict physiological effects reduced blood supply correlate these responses with observations damage. Therefore, it crucial establish detailed 3D organization vasculature, which could be used develop more accurate in silico models. To this end, we have adapted our functional ultrasound imaging platform, previously designed for recording large scale activity, enable rapid reproducible acquisition, segmentation reconstruction cortical vasculature. For first time, allows us digitize $$\sim 100$$ - $$\mu $$ m3 spatial resolution. Unlike most available strategies, approach can performed vivo within minutes. Moreover, easy implement since requires neither exogenous contrast agents nor long post-processing time. cortex-wide vasculature its quantitative analysis, including i) classification descending arteries versus ascending than 1500 vessels/animal ii) estimation their length. Importantly, confirmed relevance model stroke, visualization ischemic lesion. This development contributes extending capabilities neuroimaging better understand such as cognitive impairment tumors, highly scalable clinic.

Language: Английский

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Quantitative CT imaging characteristics of patients with chronic obstructive pulmonary disease with different eosinophil levels: a retrospective observational study using linked data from a tertiary hospital in China

BMJ Open, Journal Year: 2025, Volume and Issue: 15(2), P. e088887 - e088887

Published: Feb. 1, 2025

Objective To investigate the relationship between eosinophil (EOS) and CT imaging, we quantitatively evaluated bronchial wall thickening, emphysema index (EI) pulmonary vascular parameters in patients with chronic obstructive disease (COPD) based on different EOS levels. Design Retrospective observational study. Setting A tertiary hospital China. Participants 448 COPD from January 2020 to 2023. Main outcome measures Laboratory data, chest function levels: <150/µL, ≥150/µL; <100/µL, 100–300/µL, ≥300/µL; <2%, ≥2%. Results We records of diagnosed COPD. The prevalence eosinophilia ≥2% was 41.1% (184 cases), 33.7% (151 cases) ≥150/µL 9.4% (42 ≥300/µL. lower (EOS <2% or <150/µL) associated heart disease. neutrophil count percentage were significantly higher relatively group <150/µL <100/µL). When groups divided two cut-off values 2% 150/µL absolute value, no statistical significance observed for entire lung, left right lung lobe volume, (EI), heterogeneity (HI). However, compared 100–300/µL group, EI upper ≥300/µL (0.32 vs 0.37, p<0.05). Airway thickness, area Pi10 ≥2%, than those <100/µL groups, respectively. Compared lower. According values, such as value EOS, there significant difference parameters, cross-sectional less 5 mm 2 (BV5), total blood volume (TBV), BV5/TBV, network length, branchpoints endpoints (p>0.05 both). per cent predicted diffusing capacity carbon monoxide (DLCO%) that group. had residual ratio forced vital DLCO%. expiratory 1 s, maximal flow at 75%/50%/25% (MEF75%,MEF50%, MEF25%) DLCO% Conclusions Hypereosinophilic ≥300/µL) appears have thickening better function. Notably, ≥300/µL, is reduced. These findings provide valuable insights into role pathophysiology.

Language: Английский

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Predicting Stroke Through Retinal Graphs and Multimodal Self-supervised Learning

Lecture notes in computer science, Journal Year: 2025, Volume and Issue: unknown, P. 223 - 234

Published: Jan. 1, 2025

Language: Английский

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Human Cell‐Derived Matrix Composite Hydrogels with Diverse Composition for Use in Vasculature‐on‐chip Models

Advanced Healthcare Materials, Journal Year: 2024, Volume and Issue: 13(19)

Published: March 23, 2024

Microphysiological and organ-on-chip platforms seek to address critical gaps in human disease models drug development that underlie poor rates of clinical success for novel interventions. While the fabrication technology model cells used synthesize organs-on-chip have advanced considerably, most rely on animal-derived or synthetic extracellular matrix as a cell substrate, limiting mimicry physiology precluding use modeling diseases which dynamics play role pathogenesis. Here, cell-derived (hCDM) composite hydrogels 3D microphysiologic vasculature is reported. hCDM are derived from donor fibroblasts maintain complex milieu basement membrane, proteoglycans, nonfibrillar components. The 2D culture substrates demonstrated, patterned form engineered microvessels. Interestingly, enriched proteins associated with vascular morphogenesis determined by mass spectrometry, functional analysis demonstrates proangiogenic signatures endothelial cultured these hydrogels. In conclusion, this study suggests donor-derived could technical serve promote vascularization.

Language: Английский

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