Affinity-VAE for disentanglement, clustering and classification of objects in multidimensional image data

In this work we present affinity-VAE: a framework for automatic clustering and classification of objects in multidimensional image data based on their similarity. The method expands on the concept of $\beta$-VAEs with an informed similarity-based loss component driven by an affinity matrix. The affinity-VAE is able to create rotationally-invariant, morphologically homogeneous clusters in the latent representation, with improved cluster separation compared with a standard $\beta$-VAE. We explore the extent of latent disentanglement and continuity of the latent spaces on both 2D and 3D image data, including simulated biological electron cryo-tomography (cryo-ET) volumes as an example of a scientific application.

Savu: A Python-based, MPI Framework for Simultaneous Processing of Multiple, N-dimensional, Large Tomography Datasets

Diamond Light Source (DLS), the UK synchrotron facility, attracts scientists from across the world to perform ground-breaking x-ray experiments. With over 3000 scientific users per year, vast amounts of data are collected across the experimental beamlines, with the highest volume of data collected during tomographic imaging experiments. A growing interest in tomography as an imaging technique, has led to an expansion in the range of experiments performed, in addition to a growth in the size of the data per experiment. Savu is a portable, flexible, scientific processing pipeline capable of processing multiple, n-dimensional datasets in serial on a PC, or in parallel across a cluster. Developed at DLS, and successfully deployed across the beamlines, it uses a modular plugin format to enable experiment-specific processing and utilises parallel HDF5 to remove RAM restrictions. The Savu design, described throughout this paper, focuses on easy integration of existing and new functionality, flexibility and ease of use for users and developers alike.

Hierarchical Piecewise-Constant Super-regions

Recent applications in computer vision have come to heavily rely on superpixel over-segmentation as a pre-processing step for higher level vision tasks, such as object recognition, image labelling or image segmentation. Here we present a new superpixel algorithm called Hierarchical Piecewise-Constant Super-regions (HPCS), which not only obtains superpixels comparable to the state-of-the-art, but can also be applied hierarchically to form what we call n-th order super-regions. In essence, a Markov Random Field (MRF)-based anisotropic denoising formulation over the quantized feature space is adopted to form piecewise-constant image regions, which are then combined with a graph-based split & merge post-processing step to form superpixels. The graph and quantized feature based formulation of the problem allows us to generalize it hierarchically to preserve boundary adherence with fewer superpixels. Experimental results show that, despite the simplicity of our framework, it is able to provide high quality superpixels, and to hierarchically apply them to form layers of over-segmentation, each with a decreasing number of superpixels, while maintaining the same desired properties (such as adherence to strong image edges). The algorithm is also memory efficient and has a low computational cost.