Deep-FExt: Deep Feature Extraction for Vessel Segmentation and Centerline Prediction

Feature extraction is a very crucial task in image and pixel (voxel) classification and regression in biomedical image modeling. In this work we present a machine learning based feature extraction scheme based on inception models for pixel classification tasks. We extract features under multi-scale and multi-layer schemes through convolutional operators. Layers of Fully Convolutional Network are later stacked on this feature extraction layers and trained end-to-end for the purpose of classification. We test our model on the DRIVE and STARE public data sets for the purpose of segmentation and centerline detection and it out performs most existing hand crafted or deterministic feature schemes found in literature. We achieve an average maximum Dice of 0.85 on the DRIVE data set which out performs the scores from the second human annotator of this data set. We also achieve an average maximum Dice of 0.85 and kappa of 0.84 on the STARE data set. Though these datasets are mainly 2-D we also propose ways of extending this feature extraction scheme to handle 3-D datasets.Comment: 9 page

Multitemporal Fusion for the Detection of Static Spatial Patterns in Multispectral Satellite Images--with Application to Archaeological Survey

We evaluate and further develop a multitemporal fusion strategy that we use to detect the location of ancient settlement sites in the Near East and to map their distribution, a spatial pattern that remains static over time. For each ASTER images that has been acquired in our survey area in north-eastern Syria, we use a pattern classification strategy to map locations with a multispectral signal similar to the one from (few) known archaeological sites nearby. We obtain maps indicating the presence of anthrosol – soils that formed in the location of ancient settlements and that have a distinct spectral pattern under certain environmental conditions – and find that pooling the probability maps from all available time points reduces the variance of the spatial anthrosol pattern significantly. Removing biased classification maps – i.e. those that rank last when comparing the probability maps with the (limited) ground truth we have – reduces the overall prediction error even further, and we estimate optimal weights for each image using a non-negative least squares regression strategy. The ranking and pooling strategy approach we propose in this study shows a significant improvement over the plain averaging of anthrosol probability maps that we used in an earlier attempt to map archaeological sites in a 20,000 km2 area in northern Mesopotamia, and we expect it to work well in other surveying tasks that aim at mapping static surface patterns with limited ground truth in long series of multispectral images.Anthropolog

Efficient Algorithms for Moral Lineage Tracing

Lineage tracing, the joint segmentation and tracking of living cells as they move and divide in a sequence of light microscopy images, is a challenging task. Jug et al. have proposed a mathematical abstraction of this task, the moral lineage tracing problem (MLTP), whose feasible solutions define both a segmentation of every image and a lineage forest of cells. Their branch-and-cut algorithm, however, is prone to many cuts and slow convergence for large instances. To address this problem, we make three contributions: (i) we devise the first efficient primal feasible local search algorithms for the MLTP, (ii) we improve the branch-and-cut algorithm by separating tighter cutting planes and by incorporating our primal algorithms, (iii) we show in experiments that our algorithms find accurate solutions on the problem instances of Jug et al. and scale to larger instances, leveraging moral lineage tracing to practical significance.Comment: Accepted at ICCV 201

Spatio-Temporal Video Segmentation with Shape Growth or Shrinkage Constraint

We propose a new method for joint segmentation of monotonously growing or shrinking shapes in a time sequence of noisy images. The task of segmenting the image time series is expressed as an optimization problem using the spatio-temporal graph of pixels, in which we are able to impose the constraint of shape growth or of shrinkage by introducing monodirectional infinite links connecting pixels at the same spatial locations in successive image frames. The globally optimal solution is computed with a graph cut. The performance of the proposed method is validated on three applications: segmentation of melting sea ice floes and of growing burned areas from time series of 2D satellite images, and segmentation of a growing brain tumor from sequences of 3D medical scans. In the latter application, we impose an additional intersequences inclusion constraint by adding directed infinite links between pixels of dependent image structures