The throughput of electron microscopes has increased significantly in recent years, enabling detailed analysis of cell morphology and ultrastructure in fairly large tissue volumes. Analysis of neural circuits at single-synapse resolution remains the flagship target of this technique, but applications to cell and developmental biology are also starting to emerge at scale. On the light microscopy side, continuous development of light-sheet microscopes has led to a rapid increase in imaged volume dimensions, making Terabyte-scale acquisitions routine in the field.The amount of data acquired in such studies makes manual instance segmentation, a fundamental step in many analysis pipelines, impossible. While automatic segmentation approaches have improved significantly thanks to the adoption of convolutional neural networks, their accuracy still lags behind human annotations and requires additional manual proof-reading. A major hindrance to further improvements is the limited field of view of the segmentation networks preventing them from learning to exploit the expected cell morphology or other prior biological knowledge which humans use to inform their segmentation decisions. In this contribution, we show how such domain-specific information can be leveraged by expressing it as longrange interactions in a graph partitioning problem known as the lifted multicut problem. Using this formulation, we demonstrate significant improvement in segmentation accuracy for four challenging boundary-based segmentation problems from neuroscience and developmental biology.
The remarkable performance of Convolutional Neural Networks on image segmentation tasks comes at the cost of a large amount of pixelwise annotated images that have to be segmented for training. In contrast, feature-based learning methods, such as the Random Forest, require little training data, but rarely reach the segmentation accuracy of CNNs. This work bridges the two approaches in a transfer learning setting. We show that a CNN can be trained to correct the errors of the Random Forest in the source domain and then be applied to correct such errors in the target domain without retraining, as the domain shift between the Random Forest predictions is much smaller than between the raw data. By leveraging a few brushstrokes as annotations in the target domain, the method can deliver segmentations that are sufficiently accurate to act as pseudo-labels for target-domain CNN training. We demonstrate the performance of the method on several datasets with the challenging tasks of mitochondria, membrane and nuclear segmentation. It yields excellent performance compared to microscopy domain adaptation baselines, especially when a significant domain shift is involved.
The remarkable performance of Convolutional Neural Networks on image segmentation tasks comes at the cost of a large amount of pixelwise annotated images that have to be segmented for training. In contrast, feature-based learning methods, such as the Random Forest, require little training data, but never reach the segmentation accuracy of CNNs. This work bridges the two approaches in a transfer learning setting. We show that a CNN can be trained to correct the errors of the Random Forest in the source domain and then be applied to correct such errors in the target domain without retraining, as the domain shift between the Random Forest predictions is much smaller than between the raw data. By leveraging a few brushstrokes as annotations in the target domain, the method can deliver segmentations that are sufficiently accurate to act as pseudo-labels for target-domain CNN training. We demonstrate the performance of the method on several datasets with the challenging tasks of mitochondria, membrane and nuclear segmentation. It yields excellent performance compared to microscopy domain adaptation baselines, especially when a significant domain shift is involved.
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