Persistent Homology With Improved Locality Information for More Effective Delineation.

Persistent Homology (PH) has been successfully used to train networks to detect curvilinear structures and to improve the topological quality of their results. However, existing methods are very global and ignore the location of topological features. In this paper, we remedy this by introducing a new filtration function that fuses two earlier approaches: thresholding-based filtration, previously used to train deep networks to segment medical images, and filtration with height functions, typically used to compare 2D and 3D shapes. We experimentally demonstrate that deep networks trained using our PH-based loss function yield reconstructions of road networks and neuronal processes that reflect ground-truth connectivity better than networks trained with existing loss functions based on PH.

Adjusting the Ground Truth Annotations for Connectivity-Based Learning to Delineate.

Deep learning-based approaches to delineating 3D structure depend on accurate annotations to train the networks. Yet in practice, people, no matter how conscientious, have trouble precisely delineating in 3D and on a large scale, in part because the data is often hard to interpret visually and in part because the 3D interfaces are awkward to use. In this paper, we introduce a method that explicitly accounts for annotation inaccuracies. To this end, we treat the annotations as active contour models that can deform themselves while preserving their topology. This enables us to jointly train the network and correct potential errors in the original annotations. The result is an approach that boosts performance of deep networks trained with potentially inaccurate annotations.

Promoting Connectivity of Network-Like Structures by Enforcing Region Separation.

We propose a novel, connectivity-oriented loss function for training deep convolutional networks to reconstruct network-like structures, like roads and irrigation canals, from aerial images. The main idea behind our loss is to express the connectivity of roads, or canals, in terms of disconnections that they create between background regions of the image. In simple terms, a gap in the predicted road causes two background regions, that lie on the opposite sides of a ground truth road, to touch in prediction. Our loss function is designed to prevent such unwanted connections between background regions, and therefore close the gaps in predicted roads. It also prevents predicting false positive roads and canals by penalizing unwarranted disconnections of background regions. In order to capture even short, dead-ending road segments, we evaluate the loss in small image crops. We show, in experiments on two standard road benchmarks and a new data set of irrigation canals, that convnets trained with our loss function recover road connectivity so well that it suffices to skeletonize their output to produce state of the art maps. A distinct advantage of our approach is that the loss can be plugged in to any existing training setup without further modifications.

A convolutional neural network segments yeast microscopy images with high accuracy.

The identification of cell borders ('segmentation') in microscopy images constitutes a bottleneck for large-scale experiments. For the model organism Saccharomyces cerevisiae, current segmentation methods face challenges when cells bud, crowd, or exhibit irregular features. We present a convolutional neural network (CNN) named YeaZ, the underlying training set of high-quality segmented yeast images (>10 000 cells) including mutants, stressed cells, and time courses, as well as a graphical user interface and a web application ( www.quantsysbio.com/data-and-software ) to efficiently employ, test, and expand the system. A key feature is a cell-cell boundary test which avoids the need for fluorescent markers. Our CNN is highly accurate, including for buds, and outperforms existing methods on benchmark images, indicating it transfers well to other conditions. To demonstrate how efficient large-scale image processing uncovers new biology, we analyze the geometries of ≈2200 wild-type and cyclin mutant cells and find that morphogenesis control occurs unexpectedly early and gradually.

Joint Segmentation and Path Classification of Curvilinear Structures.

Detection of curvilinear structures in images has long been of interest. One of the most challenging aspects of this problem is inferring the graph representation of the curvilinear network. Most existing delineation approaches first perform binary segmentation of the image and then refine it using either a set of hand-designed heuristics or a separate classifier that assigns likelihood to paths extracted from the pixel-wise prediction. In our work, we bridge the gap between segmentation and path classification by training a deep network that performs those two tasks simultaneously. We show that this approach is beneficial because it enforces consistency across the whole processing pipeline. We apply our approach on roads and neurons datasets.

Tracing in 2D to reduce the annotation effort for 3D deep delineation of linear structures.

The difficulty of obtaining annotations to build training databases still slows down the adoption of recent deep learning approaches for biomedical image analysis. In this paper, we show that we can train a Deep Net to perform 3D volumetric delineation given only 2D annotations in Maximum Intensity Projections (MIP) of the training volumes. This significantly reduces the annotation time: We conducted a user study that suggests that annotating 2D projections is on average twice as fast as annotating the original 3D volumes. Our technical contribution is a loss function that evaluates a 3D prediction against annotations of 2D projections. It is inspired by space carving, a classical approach to reconstructing complex 3D shapes from arbitrarily-positioned cameras. It can be used to train any deep network with volumetric output, without the need to change the network's architecture. Substituting the loss is all it takes to enable 2D annotations in an existing training setup. In extensive experiments on 3D light microscopy images of neurons and retinal blood vessels, and on Magnetic Resonance Angiography (MRA) brain scans, we show that, when trained on projection annotations, deep delineation networks perform as well as when they are trained using costlier 3D annotations.