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.
Segmentation in volume EM is a semantic segmentation problem where each pixel is to be assigned the appropriate class label. The current state-of-the-art is largely based on extracting features in the encoder through various convolution and pooling stages and returning to a segmentation at the original resolution through the decoder with skip-connections @cite_0 @cite_10 @cite_4 . shorten this: most work in segmentation just uses U-Net
@cite_0 @cite_10 @cite_4
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Semantic segmentation has been a long standing challenging task in computer vision. It aims at assigning a label to each image pixel and needs a significant number of pixel-level annotated data, which is often unavailable. To address this lack of annotations, in this paper, we leverage, on one hand, a massive amount of available unlabeled or weakly labeled data, and on the other hand, non-real images created through Generative Adversarial Networks. In particular, we propose a semi-supervised framework – based on Generative Adversarial Networks (GANs) – which consists of a generator network to provide extra training examples to a multi-class classifier, acting as discriminator in the GAN framework, that assigns sample a label y from the K possible classes or marks it as a fake sample (extra class). The underlying idea is that adding large fake visual data forces real samples to be close in the feature space, which, in turn, improves multiclass pixel classification. To ensure a higher quality of generated images by GANs with consequently improved pixel classification, we extend the above framework by adding weakly annotated data, i.e., we provide class level information to the generator. We test our approaches on several challenging benchmarking visual datasets, i.e. PASCAL, SiftFLow, Stanford and CamVid, achieving competitive performance compared to state-of-the-art semantic segmentation methods. We address the problems of contour detection, bottom-up grouping and semantic segmentation using RGB-D data. We focus on the challenging setting of cluttered indoor scenes, and evaluate our approach on the recently introduced NYU-Depth V2 (NYUD2) dataset [27]. We propose algorithms for object boundary detection and hierarchical segmentation that generalize the gPb-ucm approach of [2] by making effective use of depth information. We show that our system can label each contour with its type (depth, normal or albedo). We also propose a generic method for long-range amodal completion of surfaces and show its effectiveness in grouping. We then turn to the problem of semantic segmentation and propose a simple approach that classifies super pixels into the 40 dominant object categories in NYUD2. We use both generic and class-specific features to encode the appearance and geometry of objects. We also show how our approach can be used for scene classification, and how this contextual information in turn improves object recognition. In all of these tasks, we report significant improvements over the state-of-the-art. We address the task of learning a semantic segmentation from weakly supervised data. Our aim is to devise a system that predicts an object label for each pixel by making use of only image level labels during training – the information whether a certain object is present or not in the image. Such coarse tagging of images is faster and easier to obtain as opposed to the tedious task of pixelwise labeling required in state of the art systems. We cast this task naturally as a multiple instance learning (MIL) problem. We use Semantic Texton Forest (STF) as the basic framework and extend it for the MIL setting. We make use of multitask learning (MTL) to regularize our solution. Here, an external task of geometric context estimation is used to improve on the task of semantic segmentation. We report experimental results on the MSRC21 and the very challenging VOC2007 datasets. On MSRC21 dataset we are able, by using 276 weakly labeled images, to achieve the performance of a supervised STF trained on pixelwise labeled training set of 56 images, which is a significant reduction in supervision needed. We consider the task of learning a classifier for semantic segmentation using weak supervision in the form of image labels specifying objects present in the image. Our method uses deep convolutional neural networks (cnns) and adopts an Expectation-Maximization (EM) based approach. We focus on the following three aspects of EM: (i) initialization; (ii) latent posterior estimation (E-step) and (iii) the parameter update (M-step). We show that saliency and attention maps, bottom-up and top-down cues respectively, of images with single objects (simple images) provide highly reliable cues to learn an initialization for the EM. Intuitively, given weak supervisions, we first learn to segment simple images and then move towards the complex ones. Next, for updating the parameters (M step), we propose to minimize the combination of the standard softmax loss and the KL divergence between the latent posterior distribution (obtained using the E-step) and the likelihood given by the cnn. This combination is more robust to wrong predictions made by the E step of the EM algorithm. Extensive experiments and discussions show that our method is very simple and intuitive, and outperforms the state-of-the-art method with a very high margin of 3.7 and 3.9 on the PASCAL VOC12 train and test sets respectively, thus setting new state-of-the-art results.