New methods for the geometrical analysis of tubular organs

Grélard, Florent; Baldacci, Fabien; Vialard, Anne; Domenger, Jean‐Philippe

doi:10.1016/j.media.2017.07.008

Cited by 25 publications

(15 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The deletion of such short junctions is a commonly described issue when working with skeletons (e.g. Barry, Chan, & Williams, ; Grélard et al, ). To delete such junctions, geodesic distance transform (MATLAB function “bwdistgeodesic”) was used, which can measure the distance between a pair of voxels obtained by traversing only the foreground voxels.…”

Section: Data Processingmentioning

confidence: 99%

See 1 more Smart Citation

An X‐ray microtomography‐based method for detailed analysis of the three‐dimensional morphology of fungal pellets

Schmideder

Barthel

Friedrich

et al. 2019

Biotech & Bioengineering

View full text Add to dashboard Cite

Filamentous fungi are widely used in the production of biotechnological compounds.Since their morphology is strongly linked to productivity, it is a key parameter in industrial biotechnology. However, identifying the morphological properties of filamentous fungi is challenging. Owing to a lack of appropriate methods, the detailed three-dimensional morphology of filamentous pellets remains unexplored. In the present study, we used state-of-the-art X-ray microtomography (µCT) to develop a new method for detailed characterization of fungal pellets. µCT measurements were performed using freeze-dried pellets obtained from submerged cultivations. Threedimensional images were generated and analyzed to locate and quantify hyphal material, tips, and branches. As a result, morphological properties including hyphal length, tip number, branch number, hyphal growth unit, porosity, and hyphal average diameter were ascertained. To validate the potential of the new method, two fungal pellets were studied-one from Aspergillus niger and the other from Penicillium chrysogenum. We show here that µCT analysis is a promising tool to study the threedimensional structure of pellet-forming filamentous microorganisms in utmost detail.The knowledge gained can be used to understand and thus optimize pellet structures by means of appropriate process or genetic control in biotechnological applications. K E Y W O R D Sfilamentous fungi, image analysis, pellets, three-dimensional morphological quantification, X-ray microtomography

show abstract

Section: Data Processingmentioning

confidence: 99%

“…,b). The deletion of such short junctions is a commonly described issue when working with skeletons (e.g Barry, Chan, & Williams, 2009;Grélard et al, 2017)…”

mentioning

confidence: 99%

An X‐ray microtomography‐based method for detailed analysis of the three‐dimensional morphology of fungal pellets

Schmideder

Barthel

Friedrich

et al. 2019

Biotech & Bioengineering

View full text Add to dashboard Cite

show abstract

“…For each path we corrected for the discretization error -a process known as re-centring. 24 We implemented a similar method to that described by Irving et al 30 A five point smoothing was performed along each path. We modelled the centreline as a continuous model by fitting a cubic spline F : [0, k n ] → R 3 denoted as…”

Section: Recentring and Spline Fittingmentioning

confidence: 99%

Reproducibility of an airway tapering measurement in computed tomography with application to bronchiectasis

et al. 2019

View full text Add to dashboard Cite

Purpose: This paper proposes a pipeline to acquire a scalar tapering measurement from the carina to the most distal point of an individual airway visible on CT. We show the applicability of using tapering measurements on clinically acquired data by quantifying the reproducibility of the tapering measure. Methods: We generate a spline from the centreline of an airway to measure the area and arclength at contiguous intervals. The tapering measurement is the gradient of the linear regression between area in log space and arclength. The reproducibility of the measure was assessed by analysing different radiation doses, voxel sizes and reconstruction kernel on single timepoint and longitudinal CT scans and by evaluating the effct of airway bifurcations. Results: Using 74 airways from 10 CT scans, we show a statistical difference, p = 3.4 × 10 −4 in tapering between healthy airways (n = 35) and those affected by bronchiectasis (n = 39). The difference between the mean of the two populations was 0.011mm −1 and the difference between the medians of the two populations was 0.006mm −1 . The tapering measurement retained a 95% confidence interval of ±0.005mm −1 in a simulated 25 mAs scan and retained a 95% confidence of ±0.005mm −1 on simulated CTs up to 1.5 times the original voxel size. Conclusion: We have established an estimate of the precision of the tapering measurement and estimated the effect on precision of simulated voxel size and CT scan dose. We recommend that the scanner calibration be undertaken with the phantoms as described, on the specific CT scanner, radiation dose and reconstruction algorithm that is to be used in any quantitative studies.Our code is available at https://github.com/quan14/AirwayTaperingInCT

show abstract

“…The centreline was corrected for any discretization errors, a process known as re-centring. 15 In this study, a five-point smoothing approach was adopted on each point on the centreline. Next, we require a continuous model to compute the tangent along the airway.…”

Section: Centrelinementioning

confidence: 99%

Tapering analysis of airways with bronchiectasis

Quan

Shipley

Tanno

et al. 2018

Medical Imaging 2018: Image Processing

View full text Add to dashboard Cite

Bronchiectasis is the permanent dilation of airways. Patients with the disease can suffer recurrent exacerbations, reducing their quality of life. The gold standard to diagnose and monitor bronchiectasis is accomplished by inspection of chest computed tomography (CT) scans. A clinician examines the broncho-arterial ratio to determine if an airway is brochiectatic. The visual analysis assumes the blood vessel diameter remains constant, although this assumption is disputed in the literature. We propose a simple measurement of tapering along the airways to diagnose and monitor bronchiectasis. To this end, we constructed a pipeline to measure the cross-sectional area along the airways at contiguous intervals, starting from the carina to the most distal point observable. Using a phantom with calibrated 3D printed structures, the precision and accuracy of our algorithm extends to the sub voxel level. The tapering measurement is robust to bifurcations along the airway and was applied to chest CT images acquired in clinical practice. The result is a statistical difference in tapering rate between airways with bronchiectasis and controls.

show abstract

New methods for the geometrical analysis of tubular organs

Cited by 25 publications

References 30 publications

An X‐ray microtomography‐based method for detailed analysis of the three‐dimensional morphology of fungal pellets

An X‐ray microtomography‐based method for detailed analysis of the three‐dimensional morphology of fungal pellets

Reproducibility of an airway tapering measurement in computed tomography with application to bronchiectasis

Tapering analysis of airways with bronchiectasis

Contact Info

Product

Resources

About