arXiv subjects

Joana Sarah Grah

Publications and source records attributed to Joana Sarah Grah.

3 recordsLinked to original sources

arXiv2018

Unified Models for Second-Order TV-Type Regularisation in Imaging - A New Perspective Based on Vector Operators

We introduce a novel regulariser based on the natural vector field operations gradient, divergence, curl and shear. For suitable choices of the weighting parameters contained in our model it generalises well-known first- and second-order TV-type regularisation methods including TV, ICTV and TGV$^2$ and enables interpolation between them. To better understand the influence of each parameter, we characterise the nullspaces of the respective regularisation functionals. Analysing the continuous model, we conclude that it is not sufficient to combine penalisation of the divergence and the curl to achieve high-quality results, but interestingly it seems crucial that the penalty functional includes at least one component of the shear or suitable boundary conditions. We investigate which requirements regarding the choice of weighting parameters yield a rotational invariant approach. To guarantee physically meaningful reconstructions, implying that conservation laws for vectorial differential operators remain valid, we need a careful discretisation that we therefore discuss in detail.

math.NA↗

arXiv2017

Learning Filter Functions in Regularisers by Minimising Quotients

Learning approaches have recently become very popular in the field of inverse problems. A large variety of methods has been established in recent years, ranging from bi-level learning to high-dimensional machine learning techniques. Most learning approaches, however, only aim at fitting parametrised models to favourable training data whilst ignoring misfit training data completely. In this paper, we follow up on the idea of learning parametrised regularisation functions by quotient minimisation as established in [3]. We extend the model therein to include higher-dimensional filter functions to be learned and allow for fit- and misfit-training data consisting of multiple functions. We first present results resembling behaviour of well-established derivative-based sparse regularisers like total variation or higher-order total variation in one-dimension. Our second and main contribution is the introduction of novel families of non-derivative-based regularisers. This is accomplished by learning favourable scales and geometric properties while at the same time avoiding unfavourable ones.

math.OC↗

arXiv2017

Mathematical Imaging Methods for Mitosis Analysis in Live-Cell Phase Contrast Microscopy

In this paper we propose a workflow to detect and track mitotic cells in time-lapse microscopy image sequences. In order to avoid the requirement for cell lines expressing fluorescent markers and the associated phototoxicity, phase contrast microscopy is often preferred over fluorescence microscopy in live-cell imaging. However, common specific image characteristics complicate image processing and impede use of standard methods. Nevertheless, automated analysis is desirable due to manual analysis being subjective, biased and extremely time-consuming for large data sets. Here, we present the following workflow based on mathematical imaging methods. In the first step, mitosis detection is performed by means of the circular Hough transform. The obtained circular contour subsequently serves as an initialisation for the tracking algorithm based on variational methods. It is sub-divided into two parts: in order to determine the beginning of the whole mitosis cycle, a backwards tracking procedure is performed. After that, the cell is tracked forwards in time until the end of mitosis. As a result, the average of mitosis duration and ratios of different cell fates (cell death, no division, division into two or more daughter cells) can be measured and statistics on cell morphologies can be obtained. All of the tools are featured in the user-friendly MATLAB$^{\circledR}$ Graphical User Interface MitosisAnalyser.

q-bio.QM↗