Carsten Haubold

Ambient point clouds for view interpolation

View interpolation and image-based rendering algorithms often produce visual artifacts in regions where the 3D scene geometry is erroneous, uncertain, or incomplete. We introduce ambient point clouds constructed from colored pixels with uncertain depth, which help reduce these artifacts while providing non-photorealistic background coloring and emphasizing reconstructed 3D geometry. Ambient point clouds are created by randomly sampling colored points along the viewing rays associated with uncertain pixels. Our real-time rendering system combines these with more traditional rigid 3D point clouds and colored surface meshes obtained using multiview stereo. Our resulting system can handle larger-range view transitions with fewer visible artifacts than previous approaches.

Graphical model for joint segmentation and tracking of multiple dividing cells

MOTIVATION To gain fundamental insight into the development of embryos, biologists seek to understand the fate of each and every embryonic cell. For the generation of cell tracks in embryogenesis, so-called tracking-by-assignment methods are flexible approaches. However, as every two-stage approach, they suffer from irrevocable errors propagated from the first stage to the second stage, here from segmentation to tracking. It is therefore desirable to model segmentation and tracking in a joint holistic assignment framework allowing the two stages to maximally benefit from each other. RESULTS We propose a probabilistic graphical model, which both automatically selects the best segments from a time series of oversegmented images/volumes and links them across time. This is realized by introducing intra-frame and inter-frame constraints between conflicting segmentation and tracking hypotheses while at the same time allowing for cell division. We show the efficiency of our algorithm on a challenging 3D+t cell tracking dataset from Drosophila embryogenesis and on a 2D+t dataset of proliferating cells in a dense population with frequent overlaps. On the latter, we achieve results significantly better than state-of-the-art tracking methods. AVAILABILITY AND IMPLEMENTATION Source code and the 3D+t Drosophila dataset along with our manual annotations will be freely available on http://hci.iwr.uni-heidelberg.de/MIP/Research/tracking/

An objective comparison of cell-tracking algorithms

We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays todays state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.

Semi-Global Matching: A Principled Derivation in Terms of Message Passing

Semi-global matching, originally introduced in the context of dense stereo, is a very successful heuristic to minimize the energy of a pairwise multi-label Markov Random Field defined on a grid. We offer the first principled explanation of this empirically successful algorithm, and clarify its exact relation to belief propagation and tree-reweighted message passing. One outcome of this new connection is an uncertainty measure for the MAP label of a variable in a Markov Random Field.

Segmenting and Tracking Multiple Dividing Targets Using ilastik

Tracking crowded cells or other targets in biology is often a challenging task due to poor signal-to-noise ratio, mutual occlusion, large displacements, little discernibility, and the ability of cells to divide. We here present an open source implementation of conservation tracking (Schiegg et al., IEEE international conference on computer vision (ICCV). IEEE, New York, pp 2928-2935, 2013) in the ilastik software framework. This robust tracking-by-assignment algorithm explicitly makes allowance for false positive detections, undersegmentation, and cell division. We give an overview over the underlying algorithm and parameters, and explain the use for a light sheet microscopy sequence of a Drosophila embryo. Equipped with this knowledge, users will be able to track targets of interest in their own data.

A Generalized Successive Shortest Paths Solver for Tracking Dividing Targets

Tracking-by-detection methods are prevailing in many tracking scenarios. One attractive property is that in the absence of additional constraints they can be solved optimally in polynomial time, e.g. by min-cost flow solvers. But when potentially dividing targets need to be tracked – as is the case for biological tasks like cell tracking – finding the solution to a global tracking-by-detection model is NP-hard. In this work, we present a flow-based approximate solution to a common cell tracking model that allows for objects to merge and split or divide. We build on the successive shortest path min-cost flow algorithm but alter the residual graph such that the flow through the graph obeys division constraints and always represents a feasible tracking solution. By conditioning the residual arc capacities on the flow along logically associated arcs we obtain a polynomial time heuristic that achieves close-to-optimal tracking results while exhibiting a good anytime performance. We also show that our method is a generalization of an approximate dynamic programming cell tracking solver by Magnusson et al. that stood out in the ISBI Cell Tracking Challenges.

Proof-reading guidance in cell tracking by sampling from tracking-by-assignment models

Automated cell tracking methods are still error-prone. On very large data sets, uncertainty measures are thus needed to guide the expert to the most ambiguous events so these can be corrected with minimal effort. We present two easy-to-use methods to sample multiple proposal solutions from a tracking-by-assignment graphical model and experimentally evaluate the benefits of the uncertainty measures derived. Expert time for proof-reading is reduced greatly compared to random selection of predicted events.

DiversePathsJ: diverse shortest paths for bioimage analysis

Motivation We introduce a formulation for the general task of finding diverse shortest paths between two end‐points. Our approach is not linked to a specific biological problem and can be applied to a large variety of images thanks to its generic implementation as a user‐friendly ImageJ/Fiji plugin. It relies on the introduction of additional layers in a Viterbi path graph, which requires slight modifications to the standard Viterbi algorithm rules. This layered graph construction allows for the specification of various constraints imposing diversity between solutions. Results The software allows obtaining a collection of diverse shortest paths under some user‐defined constraints through a convenient and user‐friendly interface. It can be used alone or be integrated into larger image analysis pipelines. Availability and implementation http://bigwww.epfl.ch/algorithms/diversepathsj

Diverse M-Best Solutions by Dynamic Programming

Many computer vision pipelines involve dynamic programming primitives such as finding a shortest path or the minimum energy solution in a tree-shaped probabilistic graphical model. In such cases, extracting not merely the best, but the set of M-best solutions is useful to generate a rich collection of candidate proposals that can be used in downstream processing. In this work, we show how M-best solutions of tree-shaped graphical models can be obtained by dynamic programming on a special graph with M layers. The proposed multi-layer concept is optimal for searching M-best solutions, and so flexible that it can also approximate M-best diverse solutions. We illustrate the usefulness with applications to object detection, panorama stitching and centerline extraction. Note: We have observed that an assumption in section 4 of our paper is not always fulfilled, see the attached corrigendum for details.