Automated Labeling of Electron Microscopy Images Using Deep Learning
Authors: Gunther Weber (Lawrence Berkeley National Laboratory; University of California, Davis)
Abstract: Searching for scientific data requires metadata providing a relevant context. Today, generating metadata is a time and labor intensive manual process that is often neglected, and important datasets are not accessible through search. We investigate the use of machine learning to generalize metadata from a subset of labeled data, thus increasing the availability of meaningful metadata for search. Specifically, we consider electron microscopy images collected at the National Center for Electron Microscopy at the Lawrence Berkeley National Laboratory and use of deep learning to discern characteristics from a small subset of labeled images and transfer labels to the entire image corpus.
Relatively small training set sizes and a minimum resolution of 512x512 pixels required by the application domain pose unique challenges. We overcome these challenges by using a simple yet powerful convolutional network architecture that limits the number of free parameters to lower the required amount of computational power and reduce the risk of overfitting. We achieve a classification accuracy of approximately 80% in discerning between images recorded in two operating modes of the electron microscope---transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). We use transfer learning–i.e., re-using the pre-trained convolution layers from the TEM vs. STEM classification problem–to generalize labels and achieve an accuracy of approximately 70% despite current experiments being limited to small training data sets. We present these predictions as suggestions to domain scientists to accelerate the labeling process with the goal of further validating our approach and improving the accuracy of automatically created labels.
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