An Object-Based Markov Random Field with Partition-Global Alternately Updated for Semantic Segmentation of High Spatial Resolution Remote Sensing Image

The Markov random field (MRF) method is widely used in remote sensing image semantic segmentation because of its excellent spatial (relationship description) ability. However, there are some targets that are relatively small and sparsely distributed in the entire image, which makes it easy to misclassify these pixels into different classes. To solve this problem, this paper proposes an object-based Markov random field method with partition-global alternately updated (OMRF-PGAU). First, four partition images are constructed based on the original image, they overlap with each other and can be reconstructed into the original image; the number of categories and region granularity for these partition images are set. Then, the MRF model is built on the partition images and the original image, their segmentations are alternately updated. The update path adopts a circular path, and the correlation assumption is adopted to establish the connection between the label fields of partition images and the original image. Finally, the relationship between each label field is constantly updated, and the final segmentation result is output after the segmentation has converged. Experiments on texture images and different remote sensing image datasets show that the proposed OMRF-PGAU algorithm has a better segmentation performance than other selected state-of-the-art MRF-based methods.

A spatio-temporal model to reveal oscillator phenotypes in molecular clocks: Parameter estimation elucidates circadian gene transcription dynamics in single-cells

We propose a stochastic distributed delay model together with a Markov random field prior and a measurement model for bioluminescence-reporting to analyse spatio-temporal gene expression in intact networks of cells. The model describes the oscillating time evolution of molecular mRNA counts through a negative transcriptional-translational feedback loop encoded in a chemical Langevin equation with a probabilistic delay distribution. The model is extended spatially by means of a multiplicative random effects model with a first order Markov random field prior distribution. Our methodology effectively separates intrinsic molecular noise, measurement noise, and extrinsic noise and phenotypic variation driving cell heterogeneity, while being amenable to parameter identification and inference. Based on the single-cell model we propose a novel computational stability analysis that allows us to infer two key characteristics, namely the robustness of the oscillations, i.e. whether the reaction network exhibits sustained or damped oscillations, and the profile of the regulation, i.e. whether the inhibition occurs over time in a more distributed versus a more direct manner, which affects the cells’ ability to phase-shift to new schedules. We show how insight into the spatio-temporal characteristics of the circadian feedback loop in the suprachiasmatic nucleus (SCN) can be gained by applying the methodology to bioluminescence-reported expression of the circadian core clock gene Cry1 across mouse SCN tissue. We find that while (almost) all SCN neurons exhibit robust cell-autonomous oscillations, the parameters that are associated with the regulatory transcription profile give rise to a spatial division of the tissue between the central region whose oscillations are resilient to perturbation in the sense that they maintain a high degree of synchronicity, and the dorsal region which appears to phase shift in a more diversified way as a response to large perturbations and thus could be more amenable to entrainment.