Fully Automated Pulmonary Lobar Segmentation: Influence of Different Prototype Software Programs onto Quantitative Evaluation of Chronic Obstructive Lung Disease

Lim, Hyung Bin; Weinheimer, Oliver; Wielpütz, Mark O.; Dinkel, Julien; Hielscher, Thomas; Gompelmann, Daniela; Kauczor, Hans‐Ulrich; Heußel, Claus Peter

doi:10.1371/journal.pone.0151498

Cited by 35 publications

(29 citation statements)

References 38 publications

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“…Lung and emphysema segmentation were performed calculating the ESI from clinically indicated preoperative CT scans taken with mixed technical parameters. After automated lung segmentation using the YACTA-software, a threshold of -950 HU was used with a noise-correction range between -910 and-950 HU to calculate the relative amount of emphysema in % of the respective lung portion 49 . While usually global ESI was measured, only the contralateral non-affected lung side was used if one lung was severely affected from the tumor.…”

Section: Methodsmentioning

confidence: 99%

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung

Prada

Espinet

Mijosek

et al. 2020

Preprint

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47The complexity of the lung microenvironment together with changes in cellular 48 composition during disease progression make it exceptionally hard to understand the 49 molecular mechanisms leading to the development of chronic lung diseases. Although 50 recent advances in cell type resolved and single-cell sequencing approaches hold 51 great promise for studying complex diseases, their implementation greatly relies on 52 local access to fresh tissue, as traditional methods to process and store tissue do not 53 allow viable cell isolation. To overcome these hurdles, we developed a novel, versatile 54 workflow that allows long-term storage of human lung tissue with high cell viability, 55 permits thorough sample quality check before cell isolation, and is compatible with 56 next generation sequencing-based profiling, including single-cell approaches. We 57 demonstrate that cryopreservation is suitable for isolation of multiple cell types from 58 different lung locations and is applicable to both healthy and diseased tissue, including 59 COPD and tumor samples. Basal cells isolated from cryopreserved airways retain the 60 ability to differentiate, indicating that cellular identity is not altered by cryopreservation. 61 Importantly, using RNA sequencing (RNA-seq) and Illumina EPIC Array, we show that 62 genome-wide gene expression and DNA methylation signatures are preserved upon 63 cryopreservation, emphasizing the suitability of our workflow for -omics profiling of 64 human lung cells. In addition, we obtained high-quality single-cell RNA sequencing 65 data of cells isolated from cryopreserved human lung, demonstrating that 66 cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, 67 3 our cryopreservation workflow is well-suited for prospective tissue collection by 68 academic collaborators and biobanks, opening worldwide access to human tissue. 69 70

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Section: Methodsmentioning

confidence: 99%

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung

Prada

Espinet

Mijosek

et al. 2020

Preprint

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“…Alternatively, a fixed percentile value may be used in emphysema measurement and disease evaluation [8-10]. The 15th percentile point has been set as the threshold value in HU, below which 15% of voxels with the lowest density are distributed [6, 11, 12]. The 15th percentile below –950 HU correlate well with FEV 1 [9].…”

Section: Ct Quantification Of Emphysemamentioning

confidence: 99%

“…While many software programs perform these functions, the results obtained vary across software vendors. In particular, the right minor fissure, which is often incomplete and undulating in course, is a major source of variation of lobar segmentation and quantification [11]. Automated CT densitometry does show agreement with pulmonary function testing: total lung capacity (TLC) at maximum inspiration measured using automated segmentation software, computer-aided lung informatics for pathology evaluation and rating (CALIPER), has a high correlation with whole body plethysmography (correlation coefficient of 0.88, p < 0.001) [19].…”

Section: Ct Quantification Of Emphysemamentioning

confidence: 99%

Role of Quantitative Computed Tomographic Scan Analysis in Lung Volume Reduction for Emphysema

et al. 2019

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Recent advances in bronchoscopic lung volume reduction (BLVR) offer new therapeutic alternatives for patients with emphysema and hyperinflation. Endobronchial valves and coils are 2 potential BLVR techniques which have been shown to improve pulmonary function and the quality of life in patients with emphysema. Current patient selection for LVR procedures relies on 3 main inclusion criteria: low attenuation area (in %), also known as emphysema score, heterogeneity score, and fissure integrity score. Volumetric analysis in combination with densitometric analysis of the affected lung lobe or segment with quantitative CT to determine emphysema severity play an important role in treatment planning and post-operative assessment. Due to the variations in lung anatomy, manual corrections are often required to ensure successful and accurate lobe segmentation for pathological and post-treatment CT scan analysis. The advanced development and utilisation of quantitative CT do not simply represent regional changes in pulmonary function but aids in analysis for better patient selection with severe emphysema who are most likely to benefit from BLVR.

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“…Visual phenotyping, as commonly used in clinical routine, refers to a standardized semiquantitative assessment of the extent of emphysema and airway changes [10]. Imagingdriven phenotyping may help to more accurately guide specific therapy than solely relying on pulmonary function testing (PFT) [21]. It is assumed that there is an emphasis of emphysema on the upper lobes in smoking-related COPD, whereas AATD mainly involves the lower lobes.…”

Section: Introductionmentioning

confidence: 99%

Similarities in the Computed Tomography Appearance in α1-Antitrypsin Deficiency and Smoking-Related Chronic Obstructive Pulmonary Disease in a Smoking Collective

et al. 2018

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Background: Emphysematous destruction of lung parenchyma visible in computed tomography (CT) can be attributed to chronic obstructive pulmonary disease (COPD) or to α1-antitrypsin deficiency (AATD). Objectives: We evaluated if visual semiquantitative phenotyping of CT data helps identifying individuals with AATD in a group of smokers with severe emphysema and airflow limitation. Method: n = 14 patients with AATD and n = 15 with COPD and a minimum of 10 pack years underwent CT, clinical assessment, and full-body plethysmography. The extent and type of emphysema as well as large and small airway changes were rated semiquantitatively for each lobe using a standardized previously published scoring system. Lastly, a final diagnosis for each patient was proposed. Results: AATD had a significantly lower mean emphysema score than COPD, with 8.9 ± 3.4 versus 11.9 ± 3.2 (p < 0.001), respectively. Within both groups, there was significantly more emphysema in the lower lobes (p < 0.05–0.001). The COPD group showed an upper- and middle-lobe predominance of emphysema distribution when compared to the AATD group (p < 0.001). Centrilobular (CLE) and panlobular (PLE) emphysema patterns showed a uniform distribution within both groups, with a CLE predominance in the upper lung and a PLE predominance in the lower lung regions. AATD and COPD both showed significantly more airway changes in lower lobes compared to upper lobes (p = 0.05–0.001), without significant differences between both groups. Conclusion: The typical emphysema distribution patterns seen on CT traditionally assigned to AATD and COPD were of little use in discriminating both entities. Also, airway changes could not contribute to a more precise differentiation. We conclude that a concise standardized phenotyping-driven approach to chest CT in emphysema is not sufficient to identify patients with AATD in a cohort of smokers with advanced emphysema.

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Fully Automated Pulmonary Lobar Segmentation: Influence of Different Prototype Software Programs onto Quantitative Evaluation of Chronic Obstructive Lung Disease

Cited by 35 publications

References 38 publications

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung

Role of Quantitative Computed Tomographic Scan Analysis in Lung Volume Reduction for Emphysema

Similarities in the Computed Tomography Appearance in α1-Antitrypsin Deficiency and Smoking-Related Chronic Obstructive Pulmonary Disease in a Smoking Collective

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