Capturing images of documents is one of the easiest and most used methods of recording them. These images however, being captured with the help of handheld devices, often lead to undesirable distortions that are hard to remove. We propose a supervised Gated and Bifurcated Stacked U-Net module to predict a dewarping grid and create a distortion free image from the input. While the network is trained on synthetically warped document images, results are calculated on the basis of real world images. The novelty in our methods exists not only in a bifurcation of the U-Net to help eliminate the intermingling of the grid coordinates, but also in the use of a gated network which adds boundary and other minute line level details to the model. The end-to-end pipeline proposed by us achieves state-of-the-art performance on the DocUNet dataset after being trained on just 8 percent of the data used in previous methods.
Motivation
Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared with real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms.
Results
In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with ‘warp’ modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data.
Availabilityand implementation
https://github.com/xulabs/aitom.
Supplementary information
Supplementary data are available at Bioinformatics online.
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