@conference {Schlesinger2017,
	title = {Crowd sourcing image segmentation with iaSTAPLE},
	booktitle = {Proceedings - International Symposium on Biomedical Imaging},
	year = {2017},
	pages = {401{\textendash}405},
	abstract = {We propose a novel label fusion technique as well as a crowdsourcing protocol to efficiently obtain accurate epithelial cell segmentations from non-expert crowd workers. Our label fusion technique simultaneously estimates the true segmentation, the performance levels of individual crowd workers, and an image segmentation model in the form of a pairwise Markov random field. We term our approach image-aware STAPLE (iaSTAPLE) since our image segmentation model seamlessly integrates into the well-known and widely used STAPLE approach. In an evaluation on a light microscopy dataset containing more than 5000 membrane labeled epithelial cells of a fly wing, we show that iaSTAPLE outperforms STAPLE in terms of segmentation accuracy as well as in terms of the accuracy of estimated crowd worker performance levels, and is able to correctly segment 99\% of all cells when compared to expert segmentations. These results show that iaSTAPLE is a highly useful tool for crowd sourcing image segmentation.},
	keywords = {Crowdsourcing, Epithelial cell segmentation, IaSTAPLE, Markovian Random Fields},
	isbn = {9781509011711},
	issn = {19458452},
	doi = {10.1109/ISBI.2017.7950547},
	author = {Schlesinger, Dmitrij and Jug, Florian and Myers, Gene and Carsten Rother and Kainmueller, Dagmar}
}
@conference {Royer2016,
	title = {Convexity shape constraints for image segmentation},
	booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
	volume = {2016-Decem},
	year = {2016},
	month = {sep},
	pages = {402{\textendash}410},
	abstract = {Segmenting an image into multiple components is a central task in computer vision. In many practical scenarios, prior knowledge about plausible components is available. Incorporating such prior knowledge into models and algorithms for image segmentation is highly desirable, yet can be non-trivial. In this work, we introduce a new approach that allows, for the first time, to constrain some or all components of a segmentation to have convex shapes. Specifically, we extend the Minimum Cost Multicut Problem by a class of constraints that enforce convexity. To solve instances of this NP-hard integer linear program to optimality, we separate the proposed constraints in the branch-and-cut loop of a state-of-the-art ILP solver. Results on photographs and micrographs demonstrate the effectiveness of the approach as well as its advantages over the state-of-the-art heuristic.},
	isbn = {9781467388504},
	issn = {10636919},
	doi = {10.1109/CVPR.2016.50},
	url = {http://arxiv.org/abs/1509.02122},
	author = {Royer, Loic A. and Richmond, David L. and Carsten Rother and Bj{\"o}rn Andres and Kainmueller, Dagmar}
}
@conference {Richmond2016,
	title = {Mapping auto-context decision forests to deep convnets for semantic segmentation},
	booktitle = {British Machine Vision Conference 2016, BMVC 2016},
	volume = {2016-Septe},
	year = {2016},
	month = {jul},
	pages = {144.1{\textendash}144.12},
	abstract = {We consider the task of pixel-wise semantic segmentation given a small set of labeled training images. Among two of the most popular techniques to address this task are Random Forests (RF) and Neural Networks (NN). In this work, we explore the relationship between two special forms of these techniques: stacked RFs (namely Auto-context) and deep Convolutional Neural Networks (ConvNet). Our main contribution is to show that Auto-context can be mapped to a deep ConvNet with novel architecture, and thereby trained end-to-end. This mapping can be viewed as an intelligent initialization of a deep ConvNet, enabling training even in the face of very limited amounts of training data. We also demonstrate an approximate mapping back from the refined ConvNet to a second stacked RF, with improved performance over the original. We experimentally verify that these mappings outperform stacked RFs for two different applications in computer vision and biology: Kinect-based body part labeling from depth images, and somite segmentation in microscopy images of developing zebrafish.},
	doi = {10.5244/C.30.144},
	url = {http://arxiv.org/abs/1507.07583},
	author = {Richmond, David L. and Kainmueller, Dagmar and Yang, Michael Y. and Myers, Eugene W. and Carsten Rother}
}
@conference {Richmond2016a,
	title = {Mapping auto-context decision forests to deep convnets for semantic segmentation},
	booktitle = {British Machine Vision Conference 2016, BMVC 2016},
	volume = {2016-Septe},
	year = {2016},
	pages = {144.1{\textendash}144.12},
	abstract = {We consider the task of pixel-wise semantic segmentation given a small set of labeled training images. Among two of the most popular techniques to address this task are Random Forests (RF) and Neural Networks (NN). In this work, we explore the relationship between two special forms of these techniques: stacked RFs (namely Auto-context) and deep Convolutional Neural Networks (ConvNet). Our main contribution is to show that Auto-context can be mapped to a deep ConvNet with novel architecture, and thereby trained end-to-end. This mapping can be viewed as an intelligent initialization of a deep ConvNet, enabling training even in the face of very limited amounts of training data. We also demonstrate an approximate mapping back from the refined ConvNet to a second stacked RF, with improved performance over the original. We experimentally verify that these mappings outperform stacked RFs for two different applications in computer vision and biology: Kinect-based body part labeling from depth images, and somite segmentation in microscopy images of developing zebrafish.},
	doi = {10.5244/C.30.144},
	url = {https://github.com/BVLC/caffe/wiki/Model-Zoo\#fcn},
	author = {Richmond, David L and Kainmueller, Dagmar and Yang, Michael Y and Myers, Eugene W and Carsten Rother}
}
@conference {Richmond2016b,
	title = {Mapping auto-context decision forests to deep convnets for semantic segmentation},
	booktitle = {British Machine Vision Conference 2016, BMVC 2016},
	volume = {2016-Septe},
	year = {2016},
	pages = {144.1{\textendash}144.12},
	abstract = {We consider the task of pixel-wise semantic segmentation given a small set of labeled training images. Among two of the most popular techniques to address this task are Random Forests (RF) and Neural Networks (NN). In this work, we explore the relationship between two special forms of these techniques: stacked RFs (namely Auto-context) and deep Convolutional Neural Networks (ConvNet). Our main contribution is to show that Auto-context can be mapped to a deep ConvNet with novel architecture, and thereby trained end-to-end. This mapping can be viewed as an intelligent initialization of a deep ConvNet, enabling training even in the face of very limited amounts of training data. We also demonstrate an approximate mapping back from the refined ConvNet to a second stacked RF, with improved performance over the original. We experimentally verify that these mappings outperform stacked RFs for two different applications in computer vision and biology: Kinect-based body part labeling from depth images, and somite segmentation in microscopy images of developing zebrafish.},
	doi = {10.5244/C.30.144},
	author = {Richmond, David L and Kainmueller, Dagmar and Yang, Michael Y and Myers, Eugene W and Carsten Rother}
}
@incollection {Richmond2015,
	title = {Uncertainty-driven forest predictors for vertebra localization and segmentation},
	volume = {9349},
	year = {2015},
	pages = {653{\textendash}660},
	abstract = {Accurate localization, identification and segmentation of vertebrae is an important task in medical and biological image analysis. The prevailing approach to solve such a task is to first generate pixelindependent features for each vertebra, e.g. via a random forest predictor, which are then fed into an MRF-based objective to infer the optimal MAP solution of a constellation model. We abandon this static, twostage approach and mix feature generation with model-based inference in a new, more flexible, way. We evaluate our method on two data sets with different objectives. The first is semantic segmentation of a 21-part body plan of zebrafish embryos in microscopy images, and the second is localization and identification of vertebrae in benchmark human CT.},
	issn = {16113349},
	doi = {10.1007/978-3-319-24553-9_80},
	author = {Richmond, David and Kainmueller, Dagmar and Glocker, Ben and Carsten Rother and Myers, Gene}
}
@conference {Kainmueller2014,
	title = {Active graph matching for automatic joint segmentation and annotation of C. elegans},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {8673 LNCS},
	number = {PART 1},
	year = {2014},
	pages = {81{\textendash}88},
	abstract = {In this work we present a novel technique we term active graph matching, which integrates the popular active shape model into a sparse graph matching problem. This way we are able to combine the benefits of a global, statistical deformation model with the benefits of a local deformation model in form of a second-order random field. We present a new iterative energy minimization technique which achieves empirically good results. This enables us to exceed state-of-the art results for the task of annotating nuclei in 3D microscopic images of C. elegans. Furthermore with the help of the generalized Hough transform we are able to jointly segment and annotate a large set of nuclei in a fully automatic fashion for the first time. {\textcopyright} 2014 Springer International Publishing.},
	isbn = {9783319104034},
	issn = {16113349},
	doi = {10.1007/978-3-319-10404-1_11},
	author = {Kainmueller, Dagmar and Jug, Florian and Carsten Rother and Myers, Gene}
}
