Automated High-Performance Analysis of Lung Morphometry

Sallon, C.; Soulet, Denis; Provost, Pierre R.; Tremblay, Yves

doi:10.1165/rcmb.2014-0469ma

Cited by 21 publications

(27 citation statements)

References 17 publications

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“…Looking to the future, the time constraints may be circumvented by automation of the tissue section analysis. Efforts in this direction are already underway by the Tremblay group (307); however, there is most likely a long and difficult road ahead before this goal is attained to the satisfaction of the stereology community.…”

Section: Quantitative Assessment Of Lung Structurementioning

confidence: 99%

Recent advances in the mechanisms of lung alveolarization and the pathogenesis of bronchopulmonary dysplasia

Silva

Nardiello

Pozarska

et al. 2015

American Journal of Physiology-Lung Cellular and Molecular Phys

120

117

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Alveolarization is the process by which the alveoli, the principal gas exchange units of the lung, are formed. Along with the maturation of the pulmonary vasculature, alveolarization is the objective of late lung development. The terminal airspaces that were formed during early lung development are divided by the process of secondary septation, progressively generating an increasing number of alveoli that are of smaller size, which substantially increases the surface area over which gas exchange can take place. Disturbances to alveolarization occur in bronchopulmonary dysplasia (BPD), which can be complicated by perturbations to the pulmonary vasculature that are associated with the development of pulmonary hypertension. Disturbances to lung development may also occur in persistent pulmonary hypertension of the newborn in term newborn infants, as well as in patients with congenital diaphragmatic hernia. These disturbances can lead to the formation of lungs with fewer and larger alveoli and a dysmorphic pulmonary vasculature. Consequently, affected lungs exhibit a reduced capacity for gas exchange, with important implications for morbidity and mortality in the immediate postnatal period and respiratory health consequences that may persist into adulthood. It is the objective of this Perspectives article to update the reader about recent developments in our understanding of the molecular mechanisms of alveolarization and the pathogenesis of BPD.

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Section: Quantitative Assessment Of Lung Structurementioning

confidence: 99%

Recent advances in the mechanisms of lung alveolarization and the pathogenesis of bronchopulmonary dysplasia

Silva

Nardiello

Pozarska

et al. 2015

American Journal of Physiology-Lung Cellular and Molecular Phys

120

117

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“…The time cost of counting however is, next to the capability of the observer to remain undistracted during this cumbersome and repetitive task, strongly dependent on the amount of inflammatory exudates and non-parenchymal areas on the fields, since these require manual selection. Previously described automatic counting methods did not exclude non-parenchymal areas or did not discriminate between septal tissue and exudates [11,12,14]. This can bias the results of these methods.…”

Section: Plos Onementioning

confidence: 99%

“…Computerized approaches offer the possibility to increase the sampling density, at a lower time cost, and thereby improve the accuracy of the result. Some authors have developed methods to quantify structural characteristics on a complete lung slide, not requiring sampling of a set of fields [11]. However, the time cost of manually cleaning these whole lung slides from non-parenchymal areas and exudates, outbalances the accuracy gained by a sample density of 100%.…”

Section: Plos Onementioning

confidence: 99%

“…STEPanizer© is a free tool that loads test systems on digital images, but still involves manual counting [ 10 ]. More recently a system for automated high–throughput analysis of whole lung slides was described, however it requires specific software [ 11 ]. Plugins or macros for freely available software to count individual fields have also been developed [ 12 – 14 ].…”

Section: Introductionmentioning

confidence: 99%

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A semi-automated method for unbiased alveolar morphometry: Validation in a bronchopulmonary dysplasia model

et al. 2020

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Reproducible and unbiased methods to quantify alveolar structure are important for research on many lung diseases. However, manually estimating alveolar structure through stereology is time consuming and inter-observer variability is high. The objective of this work was to develop and validate a fast, reproducible and accurate (semi-)automatic alternative. A FIJI-macro was designed that automatically segments lung images to binary masks, and counts the number of test points falling on tissue and the number of intersections of the airtissue interface with a set of test lines. Manual selection remains necessary for the recognition of non-parenchymal tissue and alveolar exudates. Volume density of alveolar septa (V V sep) and mean linear intercept of the airspaces (Lm) as measured by the macro were compared to theoretical values for 11 artificial test images and to manually counted values for 17 lungs slides using linear regression and Bland-Altman plots. Inter-observer agreement between 3 observers, measuring 8 lungs both manually and automatically, was assessed using intraclass correlation coefficients (ICC). V V sep and Lm measured by the macro closely approached theoretical values for artificial test images (R 2 of 0.9750 and 0.9573 and bias of 0.34% and 8.7%). The macro data in lungs were slightly higher for V V sep and slightly lower for Lm in comparison to manually counted values (R 2 of 0.8262 and 0.8288 and bias of-6.0% and 12.1%). Visually, semi-automatic segmentation was accurate. Most importantly, manually counted V V sep and Lm had only moderate to good inter-observer agreement (ICC 0.859 and 0.643), but agreements were excellent for semi-automatically counted values (ICC 0.956 and 0.900). This semi-automatic method provides accurate and highly reproducible alveolar morphometry results. Future efforts should focus on refining methods for automatic detection of non-parenchymal tissue or exudates, and for assessment of lung structure on 3D reconstructions of lungs scanned with microCT.

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“…Since tissues stained with H&E are typically autofluorescent in the red channel, the image acquisition (Zen 2.3 acquisition software) was performed using an AlexaFluor 555 filter set to generate grayscale images. Mosaic of images were exported as BigTiff files and processed using a modified algorithm used for the morphological analysis of lung alveoli as published previously (Sallon et al 2015). Briefly, Matlab software version 2014a (Mathworks) was used to perform a distributed computing analysis of the images, and results were exported as CSV files.…”

Section: Automated High-performance Histological Analysis Of Serial Amentioning

confidence: 99%

Histomorphometric analyses of human adipose tissues using intact, flash-frozen samples

Laforest

Pelletier

Michaud

et al. 2018

Histochem Cell Biol

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Histomorphometric analyses of adipose tissue usually require formalin fixation of fresh samples. Our objective was to determine if intact, flash-frozen whole adipose tissue samples stored at - 80 °C could be used for measurements developed for fresh-fixed adipose tissues. Portions of adipose tissue samples were either formalin-fixed immediately upon sampling or flash-frozen and stored at - 80 °C and then formalin-fixed during the thawing process. Mean adipocyte diameter was measured. Immunohistochemistry was performed on additional samples to identify macrophage subtypes (M1, CD14 + and M2, CD206 +) and total (CD68 +) number. All slides were counterstained using haematoxylin and eosin (H&E). Visual inspection of H&E-stained adipose tissue slides performed in a blinded fashion showed little or no sign of cell breakage in 74% of frozen-fixed samples and in 68% of fresh-fixed samples (p > 0.5). There was no difference in the distribution frequencies of adipocyte sizes in fresh-fixed vs. frozen-fixed tissues in both depots (p > 0.9). Mean adipocyte size from frozen-fixed samples correlated significantly and positively with adipocyte size from fresh-fixed samples (r = 0.74, p < 0.0001, for both depots). The quality of staining/immunostaining and appearance of tissue architecture were comparable in fresh-fixed vs. frozen-fixed samples. In conclusion, intact flash-frozen adipose tissue samples stored at - 80 °C can be used to perform techniques conventionally applied to fresh-fixed samples. This approach allows for retrospective studies with frozen human adipose tissue samples.

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Automated High-Performance Analysis of Lung Morphometry

Cited by 21 publications

References 17 publications

Recent advances in the mechanisms of lung alveolarization and the pathogenesis of bronchopulmonary dysplasia

Recent advances in the mechanisms of lung alveolarization and the pathogenesis of bronchopulmonary dysplasia

A semi-automated method for unbiased alveolar morphometry: Validation in a bronchopulmonary dysplasia model

Histomorphometric analyses of human adipose tissues using intact, flash-frozen samples

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