Deep learning algorithms can evaluate large and complex sets of data, offering various support for medical imaging analysis. Previous works have explored applications of deep learning to measure leg lengths more efficiently. These previous studies provide evidence to suggest deep-learning algorithms can improve efficiency with high levels of accuracy and speed. In this retrospective study, we utilize deep learning-based convolutional neural networks, programmed with input from a human expert, to identify key points and measure leg length. We collected frontal computed tomography (CT) scout radiographs from pre-operative CT scans of patients undergoing evaluation for knee arthroplasty from diverse sources to both train and test the model. We prepared a DenseNet121 model to predict and identify key points, which were then used to develop patch-based models. We applied separable convolutional layers to complete the analysis. The data reflects that 1) separable convolution exhibits lower mean absolute error (MAE) and increased convergence speed as compared to global average pooling layers and 2) optimal learning rates, batch size, and patch size can be achieved to present the least MAE. Our findings provide useful information and an automated tool to assist radiologists to diagnose leg length discrepancy in clinical practice.

MOTIVATION: Recent advances in mass cytometry allow simultaneous measurements of up to 50 markers at single-cell resolution. However, the high dimensionality of mass cytometry data introduces computational challenges for automated data analysis and hinders translation of new biological understanding into clinical applications. Previous studies have applied machine learning to facilitate processing of mass cytometry data. However, manual inspection is still inevitable and becoming the barrier to reliable large-scale analysis. RESULTS: We present a new algorithm called utomated ell-type iscovery and lassification (ACDC) that fully automates the classification of canonical cell populations and highlights novel cell types in mass cytometry data. Evaluations on real-world data show ACDC provides accurate and reliable estimations compared to manual gating results. Additionally, ACDC automatically classifies previously ambiguous cell types to facilitate discovery. Our findings suggest that ACDC substantially improves both reliability and interpretability of results obtained from high-dimensional mass cytometry profiling data. AVAILABILITY AND IMPLEMENTATION: A Python package (Python 3) and analysis scripts for reproducing the results are availability on https://bitbucket.org/dudleylab/acdc . CONTACT: [email protected] or [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Quantitative shape analysis is required by a wide range of biological studies across diverse scales, ranging from molecules to cells and organisms. In particular, high-throughput and systems-level studies of biological structures and functions have started to produce large volumes of complex high-dimensional shape data. Analysis and understanding of high-dimensional biological shape data require dimension-reduction techniques. RESULTS: We have developed a technique for non-linear dimension reduction of 2D and 3D biological shape representations on their Riemannian spaces. A key feature of this technique is that it preserves distances between different shapes in an embedded low-dimensional shape space. We demonstrate an application of this technique by combining it with non-linear mean-shift clustering on the Riemannian spaces for unsupervised clustering of shapes of cellular organelles and proteins. AVAILABILITY AND IMPLEMENTATION: Source code and data for reproducing results of this article are freely available at https://github.com/ccdlcmu/shape_component_analysis_Matlab The implementation was made in MATLAB and supported on MS Windows, Linux and Mac OS. CONTACT: [email protected].

We propose an automated algorithm for segmentation of mitochondria from widefield fluorescence microscopy images for quantitative morphology characterization. Mitochondria are membrane-bound organelles that are essential to cells of higher living organisms. Reliable and precise quantitative characterization of their shape is crucial to understanding related physiology and disease mechanisms. Building upon the active-mask framework developed for segmentation of confocal fluorescence microscope images, we propose a new adaptive region-based distributing function to effectively address the problem of halo artifacts that are common in widefield fluorescence images. Such artifacts prevent the segmentation of weak features of mitochondria using existing algorithms. We compare the algorithm to the original active-mask algorithm as well as the geodesic active contour algorithm based on hand-segmented ground truth, and find that it performs significantly better both qualitatively and quantitatively.