Dataset Information

Labour-efficient in vitro lymphocyte population tracking and fate prediction using automation and manual review.

ABSTRACT: Interest in cell heterogeneity and differentiation has recently led to increased use of time-lapse microscopy. Previous studies have shown that cell fate may be determined well in advance of the event. We used a mixture of automation and manual review of time-lapse live cell imaging to track the positions, contours, divisions, deaths and lineage of 44 B-lymphocyte founders and their 631 progeny in vitro over a period of 108 hours. Using this data to train a Support Vector Machine classifier, we were retrospectively able to predict the fates of individual lymphocytes with more than 90% accuracy, using only time-lapse imaging captured prior to mitosis or death of 90% of all cells. The motivation for this paper is to explore the impact of labour-efficient assistive software tools that allow larger and more ambitious live-cell time-lapse microscopy studies. After training on this data, we show that machine learning methods can be used for realtime prediction of individual cell fates. These techniques could lead to realtime cell culture segregation for purposes such as phenotype screening. We were able to produce a large volume of data with less effort than previously reported, due to the image processing, computer vision, tracking and human-computer interaction tools used. We describe the workflow of the software-assisted experiments and the graphical interfaces that were needed. To validate our results we used our methods to reproduce a variety of published data about lymphocyte populations and behaviour. We also make all our data publicly available, including a large quantity of lymphocyte spatio-temporal dynamics and related lineage information.

SUBMITTER: Chakravorty R

PROVIDER: S-EPMC3880260 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Labour-efficient in vitro lymphocyte population tracking and fate prediction using automation and manual review.

Chakravorty Rajib R Rawlinson David D Zhang Alan A Markham John J Dowling Mark R MR Wellard Cameron C Zhou Jie H S JH Hodgkin Philip D PD

PloS one 20140103 1

Interest in cell heterogeneity and differentiation has recently led to increased use of time-lapse microscopy. Previous studies have shown that cell fate may be determined well in advance of the event. We used a mixture of automation and manual review of time-lapse live cell imaging to track the positions, contours, divisions, deaths and lineage of 44 B-lymphocyte founders and their 631 progeny in vitro over a period of 108 hours. Using this data to train a Support Vector Machine classifier, we ...[more]

PMID: 24404133

Similar Datasets

Project description:Acupuncture is commonly used to reduce pain during labour despite contradictory results. The aim of this study is to evaluate the effectiveness of acupuncture with manual stimulation and acupuncture with combined manual and electrical stimulation (electro-acupuncture) compared with standard care in reducing labour pain. Our hypothesis was that both acupuncture stimulation techniques were more effective than standard care, and that electro-acupuncture was most effective.A longitudinal randomised controlled trial. The recruitment of participants took place at the admission to the labour ward between November 2008 and October 2011 at two Swedish hospitals . 303 nulliparous women with normal pregnancies were randomised to: 40 minutes of manual acupuncture (MA), electro-acupuncture (EA), or standard care without acupuncture (SC).labour pain, assessed by Visual Analogue Scale (VAS).relaxation, use of obstetric pain relief during labour and post-partum assessments of labour pain. The sample size calculation was based on the primary outcome and a difference of 15 mm on VAS was regarded as clinically relevant, this gave 101 in each group, including a total of 303 women.Mean estimated pain scores on VAS (SC: 69.0, MA: 66.4 and EA: 68.5), adjusted for: treatment, age, education, and time from baseline, with no interactions did not differ between the groups (SC vs MA: mean difference 2.6, 95% confidence interval [CI] -1.7-6.9 and SC vs EA: mean difference 0.6 [95% CI] -3.6-4.8). Fewer number of women in the EA group used epidural analgesia (46%) than women in the MA group (61%) and SC group (70%) (EA vs SC: odds ratio [OR] 0.35; [95% CI] 0.19-0.67).Acupuncture does not reduce women's experience of labour pain, neither with manual stimulation nor with combined manual and electrical stimulation. However, fewer women in the EA group used epidural analgesia thus indicating that the effect of acupuncture with electrical stimulation may be underestimated. These findings were obtained in a context with free access to other forms of pain relief.ClinicalTrials.gov: NCT01197950.

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish sampled and tagged in the lower river and tracked as they swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.

Dataset Information

Labour-efficient in vitro lymphocyte population tracking and fate prediction using automation and manual review.

Publications

Labour-efficient in vitro lymphocyte population tracking and fate prediction using automation and manual review.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets