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Accurate detection and segmentation of single cells in three-dimensional (3D) fluorescence time-lapse images is essential for observing individual cell behaviors in large bacterial communities called biofilms. Recent progress in machine-learning-based image analysis is providing this capability with ever-increasing accuracy. Leveraging the capabilities of deep convolutional neural networks (CNNs), we recently developed bacterial cell morphometry in 3D (BCM3D), an integrated image analysis pipeline that combines deep learning with conventional image analysis to detect and segment single biofilm-dwelling cells in 3D fluorescence images. While the first release of BCM3D (BCM3D 1.0) achieved state-of-the-art 3D bacterial cell segmentation accuracies, low signal-to-background ratios (SBRs) and images of very dense biofilms remained challenging. Here, we present BCM3D 2.0 to address this challenge. BCM3D 2.0 is entirely complementary to the approach utilized in BCM3D 1.0. Instead of training CNNs to perform voxel classification, we trained CNNs to translate 3D fluorescence images into intermediate 3D image representations that are, when combined appropriately, more amenable to conventional mathematical image processing than a single experimental image. Using this approach, improved segmentation results are obtained even for very low SBRs and/or high cell density biofilm images. The improved cell segmentation accuracies in turn enable improved accuracies of tracking individual cells through 3D space and time. This capability opens the door to investigating time-dependent phenomena in bacterial biofilms at the cellular level.

Motivation Data-driven deep learning techniques usually require a large quantity of labeled training data to achieve reliable solutions in bioimage analysis. However, noisy image conditions and high cell density in bacterial biofilm images make 3D cell annotations difficult to obtain. Alternatively, data augmentation via synthetic data generation is attempted, but current methods fail to produce realistic images. Results This paper presents a bioimage synthesis and assessment workflow with application to augment bacterial biofilm images. 3D cyclic generative adversarial networks (GAN) with unbalanced cycle consistency loss functions are exploited in order to synthesize 3D biofilm images from binary cell labels. Then, a stochastic synthetic dataset quality assessment (SSQA) measure that compares statistical appearance similarity between random patches from random images in two datasets is proposed. Both SSQA scores and other existing image quality measures indicate that the proposed 3D Cyclic GAN, along with the unbalanced loss function, provides a reliably realistic (as measured by mean opinion score) 3D synthetic biofilm image. In 3D cell segmentation experiments, a GAN-augmented training model also presents more realistic signal-to-background intensity ratio and improved cell counting accuracy. Availability and Implementation https://github.com/jwang-c/DeepBiofilm. Supplementary information Supplementary data are available at Bioinformatics online.

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BackgroundWhile continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge.MethodsWe study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods.ResultsWe accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs).ConclusionOur results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.

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