Automated brightfield morphometry of 3D organoid populations by OrganoSeg.
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ABSTRACT:
SUBMITTER: Borten MA
PROVIDER: S-EPMC5871765 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Current organoid technologies require intensive manual manipulation and lack uniformity in organoid size and cell composition. We present here an automated organoid platform that generates uniform organoid precursors in high-throughput. This is achieved by templating from monodisperse Matrigel droplets and sequentially delivering them into wells using a synchronized microfluidic droplet printer. Each droplet encapsulates a certain number of cells (e.g., 1,500 cells), which statistically represent the heterogeneous cell population in a tumor section. The system produces >400-μm organoids within 1 week with both inter-organoid homogeneity and inter-patient heterogeneity. This enables automated organoid printing to obtain one organoid per well. The organoids recapitulate 97% gene mutations in the parental tumor and reflect the patient-to-patient variation in drug response and sensitivity, from which we obtained more than 80% accuracy among the 21 patients investigated. This organoid platform is anticipated to fulfill the personalized medicine goal of 1-week high-throughput screening for cancer patients.
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Project description:BackgroundExcess adiposity in children is strongly correlated with obesity-related metabolic disease in adulthood, including diabetes, cardiovascular disease, and 13 types of cancer. Despite the many long-term health risks of childhood obesity, body mass index (BMI) Z-score is typically the only adiposity marker used in pediatric studies and clinical applications. The effects of regional adiposity are not captured in a single scalar measurement, and their effects on short- and long-term metabolic health are largely unknown. However, clinicians and researchers rarely deploy gold-standard methods for measuring compartmental fat such as magnetic resonance imaging (MRI) and dual X-ray absorptiometry (DXA) on children and adolescents due to cost or radiation concerns. Three-dimensional optical (3DO) scans are relatively inexpensive to obtain and use non-invasive and radiation-free imaging techniques to capture the external surface geometry of a patient's body. This 3D shape contains cues about the body composition that can be learned from a structured correlation between 3D body shape parameters and reference DXA scans obtained on a sample population.Study aimThis study seeks to introduce a radiation-free, automated 3D optical imaging solution for monitoring body shape and composition in children aged 5-17.MethodsWe introduce an automated, linear learning method to predict total and regional body composition of children aged 5-17 from 3DO scans. We collected 145 male and 206 female 3DO scans on children between the ages of 5 and 17 with three scanners from independent manufacturers. We used an automated shape templating method first introduced on an adult population to fit a topologically consistent 60,000 vertex (60 k) mesh to 3DO scans of arbitrary scanning source and mesh topology. We constructed a parameterized body shape space using principal component analysis (PCA) and estimated a regression matrix between the shape parameters and their associated DXA measurements. We automatically fit scans of 30 male and 38 female participants from a held-out test set and predicted 12 body composition measurements.ResultsThe coefficient of determination (R2) between 3DO predicted body composition and DXA measurements was at least 0.85 for all measurements with the exception of visceral fat on 3D scan predictions. Precision error was 1-4 times larger than that of DXA. No predicted variable was significantly different from DXA measurement except for male trunk lean mass.ConclusionOptical imaging can quickly, safely, and inexpensively estimate regional body composition in children aged 5-17. Frequent repeat measurements can be taken to chart changes in body adiposity over time without risk of radiation overexposure.
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Project description: Not available
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Project description:Cell line authentication is important in the biomedical field to ensure that researchers are not working with misidentified cells. Short tandem repeat is the gold standard method, but has its own limitations, including being expensive and time-consuming. Deep neural networks achieve great success in the analysis of cellular images in a cost-effective way. However, because of the lack of centralized available datasets, whether or not cell line authentication can be replaced or supported by cell image classification is still a question. Moreover, the relationship between the incubation times and cellular images has not been explored in previous studies. In this study, we automated the process of the cell line authentication by using deep learning analysis of brightfield cell line images. We proposed a novel multi-task framework to identify cell lines from cell images and predict the duration of how long cell lines have been incubated simultaneously. Using thirty cell lines' data from the AstraZeneca Cell Bank, we demonstrated that our proposed method can accurately identify cell lines from brightfield images with a 99.8% accuracy and predicts the incubation durations for cell images with the coefficient of determination score of 0.927. Considering that new cell lines are continually added to the AstraZeneca Cell Bank, we integrated the transfer learning technique with the proposed system to deal with data from new cell lines not included in the pre-trained model. Our method achieved excellent performance with a precision of 97.7% and recall of 95.8% in the detection of 14 new cell lines. These results demonstrated that our proposed framework can effectively identify cell lines using brightfield images.
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Project description:Patient satisfaction with the shape and appearance of their nose after orthognathic surgery-based skeletofacial reconstruction is an important, but often overlooked, outcome. We assessed the nose-related outcomes through a recently developed patient-reported outcome instrument and a widely adopted 3D computer-based objective outcome instrument, to verify any correlation in the results produced by these tools. We collected FACE-Q nose appearance reports (2 scales) and 3D nasal morphometry (10 parameters) from patients with class III skeletal pattern and congenital cleft lip palate deformity (n = 23) or developmental dentofacial deformity (n = 23) after (>12 months) skeletofacial reconstruction. The cleft and dentofacial cohorts demonstrated significantly (p < 0.001) poorer satisfaction scores with regard to the FACE-Q nostrils scale than the normal age-, gender-, and ethnicity-matched subjects (n = 107), without any significant difference in FACE-Q nose scale. The cleft cohort had significantly (p < 0.001) smaller nasal length, nasal tip projection, and columellar angle and greater nasal protrusion, alar width, and columellar-labial angle values than the dentofacial and normal cohorts; however, there were no significant differences between the dentofacial versus normal cohorts. The FACE-Q nose and nostrils scales were significantly (p < 0.001; r = -0.26-0.27) correlated to the results of the 3D morphometric analysis, with regard to nasal length, alar width, columella angle, and columellar-labial angle parameters. This study revealed differences in satisfaction with the appearance of the nose according to the type of underlying deformity, and demonstrated a significant correlation (low correlation coefficients) between the patient-reports and 3D image-based outcome measure tools, which has implications for multidisciplinary-centered research, auditing, and clinical care.
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