Statistical shape models, such as Active Shape Models (ASMs), suffer from their inability to represent a large range of variations of a complex shape and to account for the large errors in detection of model points. We propose a novel method (dubbed PDM-ENLOR) that overcomes these limitations by locating each shape model point individually using an ensemble of local regression models and appearance cues from selected model points. Our method first detects a set of reference points which were selected based on their saliency during training. For each model point, an ensemble of regressors is built. From the locations of the detected reference points, each regressor infers a candidate location for that model point using local geometric constraints, encoded by a point distribution model (PDM). The final location of that point is determined as a weighted linear combination, whose coefficients are learnt from the training data, of candidates proposed from its ensemble's component regressors. We use different subsets of reference points as explanatory variables for the component regressors to provide varying degrees of locality for the models in each ensemble. This helps our ensemble model to capture a larger range of shape variations as compared to a single PDM. We demonstrate the advantages of our method on the challenging problem of segmenting gene expression images of mouse brain.

Analysis of gene expression patterns in brain images obtained from high-throughput in situ hybridization requires accurate and consistent annotations of anatomical regions/subregions. Such annotations are obtained by mapping an anatomical atlas onto the gene expression images through intensity- and/or landmark-based registration methods or deformable model-based segmentation methods. Due to the complex appearance of the gene expression images, these approaches require a pre-processing step to determine landmark correspondences in order to incorporate landmark-based geometric constraints. In this paper, we propose a novel method for landmark-constrained, intensity-based registration without determining landmark correspondences a priori. The proposed method performs dense image registration and identifies the landmark correspondences, simultaneously, using a single higher-order Markov Random Field model. In addition, a machine learning technique is used to improve the discriminating properties of local descriptors for landmark matching by projecting them in a Hamming space of lower dimension. We qualitatively show that our method achieves promising results and also compares well, quantitatively, with the expert's annotations, outperforming previous methods.

An accurate labeling of a multi-part, complex anatomical structure (e.g., brain) is required in order to compare data across images for spatial analysis. It can be achieved by fitting an object-specific geometric atlas that is constructed using a partitioned, high-resolution deformable mesh and tagging each of its polygons with a region label. Subdivision meshes have been used to construct such an atlas because they can provide a compact representation of a partitioned, multi-resolution, object-specific mesh structure using only a few control points. However, automated fitting of a subdivision mesh-based geometric atlas to an anatomical structure in an image is a difficult problem and has not been sufficiently addressed. In this paper, we propose a novel Markov Random Field-based method for fitting a planar, multi-part subdivision mesh to anatomical data. The optimal fitting of the atlas is obtained by determining the optimal locations of the control points. We also tackle the problem of landmark matching in tandem with atlas fitting by constructing a single graphical model to impose pose-invariant, landmark-based geometric constraints on atlas deformation. The atlas deformation is also governed by additional constraints imposed by the mesh's geometric properties and the object boundary. We demonstrate the potential of the proposed method on the difficult problem of segmenting a mouse brain and its interior regions in gene expression images which exhibit large intensity and shape variability. We obtain promising results when compared with manual annotations and prior methods.