3D Structure from 2D Microscopy images using Deep Learning

Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional. Recent advances in Artificial Intelligence have been applied to this problem, primarily using voxel based approaches to analyse sets of electron microscopy images. Herewe present a deep learning solution for reconstructing the protein com-plexes from a number of 2D single molecule localization microscopy images, with the solution being completely unconstrained. Our convolutional neural network coupled with a differentiable renderer predicts pose and derives a single structure. After training, the network is dis-carded, with the output of this method being a structural model which fits the data-set. We demonstrate the performance of our system on two protein complexes: CEP152 (which comprises part of the proximal toroid of the centriole) and centrioles.

Boosting in Location Space

The goal of object detection is to find objects in an image. An object detector accepts an image and produces a list of locations as $(x,y)$ pairs. Here we introduce a new concept: {\bf location-based boosting}. Location-based boosting differs from previous boosting algorithms because it optimizes a new spatial loss function to combine object detectors, each of which may have marginal performance, into a single, more accurate object detector. A structured representation of object locations as a list of $(x,y)$ pairs is a more natural domain for object detection than the spatially unstructured representation produced by classifiers. Furthermore, this formulation allows us to take advantage of the intuition that large areas of the background are uninteresting and it is not worth expending computational effort on them. This results in a more scalable algorithm because it does not need to take measures to prevent the background data from swamping the foreground data such as subsampling or applying an ad-hoc weighting to the pixels. We first present the theory of location-based boosting, and then motivate it with empirical results on a challenging data set.