In the last years, automated segmentation has become a necessary tool for volume electron microscopy (EM) imaging. So far, the best performing techniques have been largely based on fully supervised encoder-decoder CNNs, requiring a substantial amount of annotated images. Domain Adaptation (DA) aims to alleviate the annotation burden by ‘adapting’ the networks trained on existing groundtruth data (source domain) to work on a different (target) domain with as little additional annotation as possible. Most DA research is focused on the classification task, whereas volume EM segmentation remains rather unexplored. In this work, we extend recently proposed classification DA techniques to an encoder-decoder layout and propose a novel method that adds a reconstruction decoder to the classical encoder-decoder segmentation in order to align source and target encoder features. The method has been validated on the task of segmenting mitochondria in EM volumes. We have performed DA from brain EM images to HeLa cells and from isotropic FIB SEM volumes to anisotropic TEM volumes. In all cases, the proposed method has outperformed the extended classification DA techniques and the finetuning baseline. An implementation of our work can be found on https: github.com JorisRoels domain-adaptive-segmentation.
The first sentence is redundant, you say this in the paragraph above and in the intro already. I would start this paragraph with the second sentence 'The first DA method...' The first DA method for semantic segmentation was proposed in @cite_3 . It is based on classical CNN feature extractors where the last feature layer is aligned using an adversarial loss. The recent work of @cite_8 also employs domain confusion for alignment, but additionally normalizes the visual appearance of source and target data. Alternatively, the work of @cite_6 proposes shared decoders combined with MMD regularization on the final decoder activations.
@cite_6 @cite_3 @cite_8
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Deep networks such as the U-Net are outstanding at segmenting biomedical images when enough training data is available, but only then. Here we introduce a Domain Adaptation approach that relies on two coupled U-Nets that either regularize or share corresponding weights between the two streams, along with a differentiable loss function that approximates the Jaccard index, to leverage training data from one domain in which it is plentiful, to adapt the network weights in another where it is scarce. We showcase our approach for the purpose of segmenting mitochondria and synapses from electron microscopy image stacks of mouse brain, when we have enough training data for one brain region but only very little for another. In such cases, we outperform state-of-the-art Domain Adaptation methods. Fully convolutional models for dense prediction have proven successful for a wide range of visual tasks. Such models perform well in a supervised setting, but performance can be surprisingly poor under domain shifts that appear mild to a human observer. For example, training on one city and testing on another in a different geographic region and or weather condition may result in significantly degraded performance due to pixel-level distribution shift. In this paper, we introduce the first domain adaptive semantic segmentation method, proposing an unsupervised adversarial approach to pixel prediction problems. Our method consists of both global and category specific adaptation techniques. Global domain alignment is performed using a novel semantic segmentation network with fully convolutional domain adversarial learning. This initially adapted space then enables category specific adaptation through a generalization of constrained weak learning, with explicit transfer of the spatial layout from the source to the target domains. Our approach outperforms baselines across different settings on multiple large-scale datasets, including adapting across various real city environments, different synthetic sub-domains, from simulated to real environments, and on a novel large-scale dash-cam dataset. The recent advances in deep neural networks have convincingly demonstrated high capability in learning vision models on large datasets. Nevertheless, collecting expert labeled datasets especially with pixel-level annotations is an extremely expensive process. An appealing alternative is to render synthetic data (e.g., computer games) and generate ground truth automatically. However, simply applying the models learnt on synthetic images may lead to high generalization error on real images due to domain shift. In this paper, we facilitate this issue from the perspectives of both visual appearance-level and representation-level domain adaptation. The former adapts source-domain images to appear as if drawn from the "style" in the target domain and the latter attempts to learn domain-invariant representations. Specifically, we present Fully Convolutional Adaptation Networks (FCAN), a novel deep architecture for semantic segmentation which combines Appearance Adaptation Networks (AAN) and Representation Adaptation Networks (RAN). AAN learns a transformation from one domain to the other in the pixel space and RAN is optimized in an adversarial learning manner to maximally fool the domain discriminator with the learnt source and target representations. Extensive experiments are conducted on the transfer from GTA5 (game videos) to Cityscapes (urban street scenes) on semantic segmentation and our proposal achieves superior results when comparing to state-of-the-art unsupervised adaptation techniques. More remarkably, we obtain a new record: mIoU of 47.5 on BDDS (drive-cam videos) in an unsupervised setting.