Generalized nucleus segmentation techniques can contribute greatly to reducing the time to develop and validate visual biomarkers for new digital pathology datasets. We summarize the results of MoNuSeg 2018 Challenge whose objective was to develop generalizable nuclei segmentation techniques in digital pathology. The challenge was an official satellite event of the MICCAI 2018 conference in which 32 teams with more than 80 participants from geographically diverse institutes participated. Contestants were given a training set with 30 images from seven organs with annotations of 21,623 individual nuclei. A test dataset with 14 images taken from seven organs, including two organs that did not appear in the training set was released without annotations. Entries were evaluated based on average aggregated Jaccard index (AJI) on the test set to prioritize accurate instance segmentation as opposed to mere semantic segmentation. More than half the teams that completed the challenge outperformed a previous baseline. Among the trends observed that contributed to increased accuracy were the use of color normalization as well as heavy data augmentation. Additionally, fully convolutional networks inspired by variants of U-Net, FCN, and Mask-RCNN were popularly used, typically based on ResNet or VGG base architectures. Watershed segmentation on predicted semantic segmentation maps was a popular post-processing strategy. Several of the top techniques compared favorably to an individual human annotator and can be used with confidence for nuclear morphometrics.

MOTIVATION: Neural networks have been widely used to analyze high-throughput microscopy images. However, the performance of neural networks can be significantly improved by encoding known invariance for particular tasks. Highly relevant to the goal of automated cell phenotyping from microscopy image data is rotation invariance. Here we consider the application of two schemes for encoding rotation equivariance and invariance in a convolutional neural network, namely, the group-equivariant CNN (G-CNN), and a new architecture with simple, efficient conic convolution, for classifying microscopy images. We additionally integrate the 2D-discrete-Fourier transform (2D-DFT) as an effective means for encoding global rotational invariance. We call our new method the Conic Convolution and DFT Network (CFNet). RESULTS: We evaluated the efficacy of CFNet and G-CNN as compared to a standard CNN for several different image classification tasks, including simulated and real microscopy images of subcellular protein localization, and demonstrated improved performance. We believe CFNet has the potential to improve many high-throughput microscopy image analysis applications. AVAILABILITY AND IMPLEMENTATION: Source code of CFNet is available at: https://github.com/bchidest/CFNet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Estimating dense correspondence or depth information from a pair of stereoscopic images is a fundamental problem in computer vision, which finds a range of important applications. Despite intensive past research efforts in this topic, it still remains challenging to recover the depth information both reliably and efficiently, especially when the input images contain weakly textured regions or are captured under uncontrolled, real-life conditions. Striking a desired balance between computational efficiency and estimation quality, a hybrid minimum spanning tree-based stereo matching method is proposed in this paper. Our method performs efficient nonlocal cost aggregation at pixel-level and region-level, and then adaptively fuses the resulting costs together to leverage their respective strength in handling large textureless regions and fine depth discontinuities. Experiments on the standard Middlebury stereo benchmark show that the proposed stereo method outperforms all prior local and nonlocal aggregation-based methods, achieving particularly noticeable improvements for low texture regions. To further demonstrate the effectiveness of the proposed stereo method, also motivated by the increasing desire to generate expressive depth-induced photo effects, this paper is tasked next to address the emerging application of interactive depth-of-field rendering given a real-world stereo image pair. To this end, we propose an accurate thin-lens model for synthetic depth-of-field rendering, which considers the user-stroke placement and camera-specific parameters and performs the pixel-adapted Gaussian blurring in a principled way. Taking ~1.5 s to process a pair of 640×360 images in the off-line step, our system named Scribble2focus allows users to interactively select in-focus regions by simple strokes using the touch screen and returns the synthetically refocused images instantly to the user.