Self-Supervised Learning of Synapse Types from EM Images

Separating synapses into different classes based on their appearance in EM images has many applications in biology. Examples may include assigning a neurotransmitter to a particular class, or separating synapses whose strength can be modulated from those whose strength is fixed. Traditionally, this has been done in a supervised manner, giving the classification algorithm examples of the different classes. Here we instead separate synapses into classes based only on the observation that nearby synapses in the same neuron are likely more similar than synapses chosen randomly from different cells. We apply our methodology to data from {\it Drosophila}. Our approach has the advantage that the number of synapse types does not need to be known in advance. It may also provide a principled way to select ground-truth that spans the range of synapse structure.

Autoproof: Automated Segmentation Proofreading for Connectomics

Producing connectomes from electron microscopy (EM) images has historically required a great deal of human proofreading effort. This manual annotation cost is the current bottleneck in scaling EM connectomics, for example, in making larger connectome reconstructions feasible, or in enabling comparative connectomics where multiple related reconstructions are produced. In this work, we propose using the available ground-truth data generated by this manual annotation effort to learn a machine learning model to automate or optimize parts of the required proofreading workflows. We validate our approach on a recent complete reconstruction of the \emph{Drosophila} male central nervous system. We first show our method would allow for obtaining 90\% of the value of a guided proofreading workflow while reducing required cost by 80\%. We then demonstrate a second application for automatically merging many segmentation fragments to proofread neurons. Our system is able to automatically attach 200 thousand fragments, equivalent to four proofreader years of manual work, and increasing the connectivity completion rate of the connectome by 1.3\% points.

Latent Feature Representation via Unsupervised Learning for Pattern Discovery in Massive Electron Microscopy Image Volumes

We propose a method to facilitate exploration and analysis of new large data sets. In particular, we give an unsupervised deep learning approach to learning a latent representation that captures semantic similarity in the data set. The core idea is to use data augmentations that preserve semantic meaning to generate synthetic examples of elements whose feature representations should be close to one another. We demonstrate the utility of our method applied to nano-scale electron microscopy data, where even relatively small portions of animal brains can require terabytes of image data. Although supervised methods can be used to predict and identify known patterns of interest, the scale of the data makes it difficult to mine and analyze patterns that are not known a priori. We show the ability of our learned representation to enable query by example, so that if a scientist notices an interesting pattern in the data, they can be presented with other locations with matching patterns. We also demonstrate that clustering of data in the learned space correlates with biologically-meaningful distinctions. Finally, we introduce a visualization tool and software ecosystem to facilitate user-friendly interactive analysis and uncover interesting biological patterns. In short, our work opens possible new avenues in understanding of and discovery in large data sets, arising in domains such as EM analysis.