A convolutional neural network for segmentation of yeast cells without manual training annotations.

MOTIVATION: Single-cell time-lapse microscopy is a ubiquitous tool for studying the dynamics of complex cellular processes. While imaging can be automated to generate very large volumes of data, the processing of the resulting movies to extract high-quality single-cell information remains a challenging task. The development of software tools that automatically identify and track cells is essential for realizing the full potential of time-lapse microscopy data. Convolutional neural networks (CNNs) are ideally suited for such applications, but require great amounts of manually annotated data for training, a time-consuming and tedious process. RESULTS: We developed a new approach to CNN training for yeast cell segmentation based on synthetic data and present (i) a software tool for the generation of synthetic images mimicking brightfield images of budding yeast cells and (ii) a convolutional neural network (Mask R-CNN) for yeast segmentation that was trained on a fully synthetic dataset. The Mask R-CNN performed excellently on segmenting actual microscopy images of budding yeast cells, and a density-based spatial clustering algorithm (DBSCAN) was able to track the detected cells across the frames of microscopy movies. Our synthetic data creation tool completely bypassed the laborious generation of manually annotated training datasets, and can be easily adjusted to produce images with many different features. The incorporation of synthetic data creation into the development pipeline of CNN-based tools for budding yeast microscopy is a critical step toward the generation of more powerful, widely applicable and user-friendly image processing tools for this microorganism. AVAILABILITY AND IMPLEMENTATION: The synthetic data generation code can be found at https://github.com/prhbrt/synthetic-yeast-cells. The Mask R-CNN as well as the tuning and benchmarking scripts can be found at https://github.com/ymzayek/yeastcells-detection-maskrcnn. We also provide Google Colab scripts that reproduce all the results of this work. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structural similarity analysis of midfacial fractures-a feasibility study.

The structural similarity index metric is used to measure the similarity between two images. The aim here was to study the feasibility of this metric to measure the structural similarity and fracture characteristics of midfacial fractures in computed tomography (CT) datasets following radiation dose reduction, iterative reconstruction (IR) and deep learning reconstruction. Zygomaticomaxillary fractures were inflicted on four human cadaver specimen and scanned with standard and low dose CT protocols. Datasets were reconstructed using varying strengths of IR and the subsequently applying the PixelShine™ deep learning algorithm as post processing. Individual small and non-dislocated fractures were selected for the data analysis. After attenuating the osseous anatomy of interest, registration was performed to superimpose the datasets and subsequently to measure by structural image quality. Changes to the fracture characteristics were measured by comparing each fracture to the mirrored contralateral anatomy. Twelve fracture locations were included in the data analysis. The most structural image quality changes occurred with radiation dose reduction (0.980036±0.011904), whilst the effects of IR strength (0.995399±0.001059) and the deep learning algorithm (0.999996±0.000002) were small. Radiation dose reduction and IR strength tended to affect the fracture characteristics. Both the structural image quality and fracture characteristics were not affected by the use of the deep learning algorithm. In conclusion, evidence is provided for the feasibility of using the structural similarity index metric for the analysis of structural image quality and fracture characteristics.

Iterative reconstruction and deep learning algorithms for enabling low-dose computed tomography in midfacial trauma.

OBJECTIVES: The objective of this study was to quantitatively assess the image quality of Advanced Modeled Iterative Reconstruction (ADMIRE) and the PixelShine (PS) deep learning algorithm for the optimization of low-dose computed tomography protocols in midfacial trauma. STUDY DESIGN: Six fresh frozen human cadaver head specimens were scanned by computed tomography using both standard and low-dose scan protocols. Three iterative reconstruction strengths were applied to reconstruct bone and soft tissue data sets and these were subsequently applied to the PS algorithm. Signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) were calculated for each data set by using the image noise measurements of 10 consecutive image slices from a standardized region of interest template. RESULTS: The low-dose scan protocol resulted in a 61.7% decrease in the radiation dose. Radiation dose reduction significantly reduced, and iterative reconstruction and the deep learning algorithm significantly improved, the CNR for bone and soft tissue data sets. The algorithms improved image quality after substantial dose reduction. The greatest improvement in SNRs and CNRs was found using the iterative reconstruction algorithm. CONCLUSION: Both the ADMIRE and PS algorithms significantly improved image quality after substantial radiation dose reduction.