Dataset Information

ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments.

ABSTRACT: In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e.g., feature extraction or tracking). Image alignment faces two obstacles in this microscopic context: (a) highly dynamic structural changes in the sample (i.e., colony growth) and (b) an individual data set-specific sample environment which makes the application of landmarks-based alignments almost impossible. We present a computational image registration solution, we refer to as ViCAR: (Vi)sual (C)ues based (A)daptive (R)egistration, for such microfluidics experiments, consisting of (1) the detection of particular polygons (outlined and segmented ones, referred to as visual cues), (2) the adaptive retrieval of three coordinates throughout different sets of frames, and finally (3) an image registration based on the relation of these points correcting both rotation and translation. We tested ViCAR with different data sets and have found that it provides an effective spatial alignment thereby paving the way to extract temporal features pertinent to each resulting bacterial colony. By using ViCAR, we achieved an image registration with 99.9% of image closeness, based on the average rmsd of 4.10-2 pixels, and superior results compared to a state of the art algorithm.

SUBMITTER: Hattab G

PROVIDER: S-EPMC5449445 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments.

Hattab Georges G Schlüter Jan-Philip JP Becker Anke A Nattkemper Tim W TW

Frontiers in genetics 20170531

In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of <i>T</i> images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Imag ...[more]

PMID: 28620411

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Project description:PurposeDeformable image registration (DIR) is a key enabling technology in many diagnostic and therapeutic tasks, but often does not meet the required robustness and accuracy for supporting clinical tasks. This is in large part due to a lack of high-quality benchmark datasets by which new DIR algorithms can be evaluated. Our team was supported by the National Institute of Biomedical Imaging and Bioengineering to develop DIR benchmark dataset libraries for multiple anatomical sites, comprising of large numbers of highly accurate landmark pairs on matching blood vessel bifurcations. Here we introduce our lung CT DIR benchmark dataset library, which was developed to improve upon the number and distribution of landmark pairs in current public lung CT benchmark datasets.Acquisition and validation methodsThirty CT image pairs were acquired from several publicly available repositories as well as authors' institution with IRB approval. The data processing workflow included multiple steps: (1) The images were denoised. (2) Lungs, airways, and blood vessels were automatically segmented. (3) Bifurcations were directly detected on the skeleton of the segmented vessel tree. (4) Falsely identified bifurcations were filtered out using manually defined rules. (5) A DIR was used to project landmarks detected on the first image onto the second image of the image pair to form landmark pairs. (6) Landmark pairs were manually verified. This workflow resulted in an average of 1262 landmark pairs per image pair. Estimates of the landmark pair target registration error (TRE) using digital phantoms were 0.4 mm ± 0.3 mm.Data format and usage notesThe data is published in Zenodo at https://doi.org/10.5281/zenodo.8200423. Instructions for use can be found at https://github.com/deshanyang/Lung-DIR-QA.Potential applicationsThe dataset library generated in this work is the largest of its kind to date and will provide researchers with a new and improved set of ground truth benchmarks for quantitatively validating DIR algorithms within the lung.

Project description:OBJECTIVE:To compare the accuracy of different methods for image registration in image-guided adaptive brachytherapy (IGABT) for cervical cancer. METHODS:The last treatment planning CT images (CT1) and the first treatment planning CT images (CT2) were acquired from 15 patients with cervical cancer and registered with different match image qualities (retained/removed catheter source in images) and different match regions [target only (S Group)/ interested organ structure (M Group)/body (L Group)] in Velocity3.2 software. The dice similarity coefficient (DSC) between the clinical target volumes (CTV) of the CT1 and CT2 images (CTVCT1 and CTVCT2, respectively) and between the organs-at-risk (OAR) of the two imaging datasets (OARCT1 and OARCT2, respectively) were used to evaluate the image registration accuracy. RESULTS:The auto-segmentation volume of the catheter source using Velocity software based on the CT threshold was the closest to the actual volume within the CT value range of 1700-1800 HU. In the retained group, the DSC for the OARs of was better than or equal to that of the removed group, and the DSC value of the rectum was significantly improved (P < 0.05). For comparison of different match regions, the high-risk target volume (HRCTV) and the low-risk target volume (IRCTV) had the best precision for registration of the target area, which was significantly greater than that of M group and L group (P < 0.05). The M group had better registration accuracy of the target area and the best accuracy for the OARs. The DSC values of the bladder and rectum were significantly better than those of the other two groups (P < 0.05). CONCLUSIONS:The CT value range of 1700-1800 HU is optimal for automatic image segmentation using Velocity software. Automatic segmentation and shielding the volume of the catheter source can improve the image quality. We recommend the use of interested organ structures regions for image registration in image-guided adaptive brachytherapy for cervical cancer.

Project description:BACKGROUND:Clonal microbial populations often harbor rare phenotypic variants that are typically hidden within the majority of the remaining cells, but are crucial for the population's resilience to external perturbations. Persister and viable but non-culturable (VBNC) cells are two important clonal bacterial subpopulations that can survive antibiotic treatment. Both persister and VBNC cells pose a serious threat to human health. However, unlike persister cells, which quickly resume growth following drug removal, VBNC cells can remain non-growing for prolonged periods of time, thus eluding detection via traditional microbiological assays. Therefore, understanding the molecular mechanisms underlying the formation of VBNC cells requires the characterization of the clonal population with single-cell resolution. A combination of microfluidics, time-lapse microscopy, and fluorescent reporter strains offers the perfect platform for investigating individual cells while manipulating their environment. METHODS:Here, we report a novel single-cell approach to investigate VBNC cells. We perform drug treatment, bacterial culturing, and live/dead staining in series by using transcriptional reporter strains and novel adaptations to the mother machine technology. Since we track each cell throughout the experiment, we are able to quantify the size, morphology and fluorescence that each VBNC cell displayed before, during and after drug treatment. RESULTS:We show that VBNC cells are not dead or dying cells but share similar phenotypic features with persister cells, suggesting a link between these two subpopulations, at least in the Escherichia coli strain under investigation. We strengthen this link by demonstrating that, before drug treatment, both persister and VBNC cells can be distinguished from the remainder of the population by their lower fluorescence when using a reporter strain for tnaC, encoding the leader peptide of the tnaCAB operon responsible for tryptophan metabolism. CONCLUSION:Our data demonstrates the suitability of our approach for studying the physiology of non-growing cells in response to external perturbations. Our approach will allow the identification of novel biomarkers for the isolation of VBNC and persister cells and will open new opportunities to map the detailed biochemical makeup of these clonal subpopulations.

Dataset Information

ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments.

Publications

ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments.

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