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Medical Image Segmentation

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Medical Image Segmentation is a computer vision task that involves dividing an medical image into multiple segments, where each segment represents a different object or structure of interest in the image. The goal of medical image segmentation is to provide a precise and accurate representation of the objects of interest within the image, typically for the purpose of diagnosis, treatment planning, and quantitative analysis.

<span style="color:grey; opacity: 0.6">( Image credit: IVD-Net )</span>

기법

관련 논문에서 소개한 기법입니다. 이 태스크에서의 평가 여부는 평가 결과에서 확인하세요.

RoIAlign

Region of Interest Align, or RoIAlign, is an operation for extracting a small feature map from each RoI in detection and segmentation based tasks. It removes the harsh quantization of RoI Pool, properly aligning the extracted features with the input. To avoid any quantization of the RoI boundaries or bins (using $x/16$ instead of $[x/16]$), RoIAlign uses bilinear interpolation to compute the exact values of the input features at four regularly sampled locations in each RoI bin, and the result is then aggregated (using max or average).

Mask R-CNN

Dense Block

A Dense Block is a module used in convolutional neural networks that connects all layers (with matching feature-map sizes) directly with each other. It was originally proposed as part of the DenseNet architecture. To preserve the feed-forward nature, each layer obtains additional inputs from all preceding layers and passes on its own feature-maps to all subsequent layers. In contrast to ResNets, we never combine features through summation before they are passed into a layer; instead, we combine features by concatenating them. Hence, the $\ell^{th}$ layer has $\ell$ inputs, consisting of the feature-maps of all preceding convolutional blocks. Its own feature-maps are passed on to all $L-\ell$ subsequent layers. This introduces $\frac{L(L+1)}{2}$ connections in an $L$-layer network, instead of just $L$, as in traditional architectures: "dense connectivity".

Densely Connected Convolutional Networks

Mask R-CNN

Mask R-CNN extends Faster R-CNN to solve instance segmentation tasks. It achieves this by adding a branch for predicting an object mask in parallel with the existing branch for bounding box recognition. In principle, Mask R-CNN is an intuitive extension of Faster R-CNN, but constructing the mask branch properly is critical for good results. Most importantly, Faster R-CNN was not designed for pixel-to-pixel alignment between network inputs and outputs. This is evident in how RoIPool, the de facto core operation for attending to instances, performs coarse spatial quantization for feature extraction. To fix the misalignment, Mask R-CNN utilises a simple, quantization-free layer, called RoIAlign, that faithfully preserves exact spatial locations. Secondly, Mask R-CNN decouples mask and class prediction: it predicts a binary mask for each class independently, without competition among classes, and relies on the network's RoI classification branch to predict the category. In contrast, an FCN usually perform per-pixel multi-class categorization, which couples segmentation and classification.

Mask R-CNN

SegNet

SegNet is a semantic segmentation model. This core trainable segmentation architecture consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network. The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification. The novelty of SegNet lies is in the manner in which the decoder upsamples its lower resolution input feature maps. Specifically, the decoder uses pooling indices computed in the max-pooling step of the corresponding encoder to perform non-linear upsampling.

SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation

Pyramid Pooling Module

A Pyramid Pooling Module is a module for semantic segmentation which acts as an effective global contextual prior. The motivation is that the problem of using a convolutional network like a ResNet is that, while the receptive field is already larger than the input image, the empirical receptive field is much smaller than the theoretical one especially on high-level layers. This makes many networks not sufficiently incorporate the momentous global scenery prior. The PPM is an effective global prior representation that addresses this problem. It contains information with different scales and varying among different sub-regions. Using our 4-level pyramid, the pooling kernels cover the whole, half of, and small portions of the image. They are fused as the global prior. Then we concatenate the prior with the original feature map in the final part.

Pyramid Scene Parsing Network

PSPNet

PSPNet, or Pyramid Scene Parsing Network, is a semantic segmentation model that utilises a pyramid parsing module that exploits global context information by different-region based context aggregation. The local and global clues together make the final prediction more reliable. We also propose an optimization Given an input image, PSPNet use a pretrained CNN with the dilated network strategy to extract the feature map. The final feature map size is $1/8$ of the input image. On top of the map, we use the pyramid pooling module to gather context information. Using our 4-level pyramid, the pooling kernels cover the whole, half of, and small portions of the image. They are fused as the global prior. Then we concatenate the prior with the original feature map in the final part of. It is followed by a convolution layer to generate the final prediction map.

Pyramid Scene Parsing Network

CPN

The Contour Proposal Network (CPN) detects possibly overlapping objects in an image while simultaneously fitting pixel-precise closed object contours. The CPN can incorporate state of the art object detection architectures as backbone networks into a fast single-stage instance segmentation model that can be trained end-to-end.

Contour Proposal Networks for Biomedical Instance Segmentation

SSDS

The method exploits the finding that high correlation of segmentation performance among each U-Net's decoder layer -- with discriminative layer attached -- tends to have higher segmentation performance in the final segmentation map. By introducing an "Inter-layer Divergence Loss", based on Kulback-Liebler Divergence, to promotes the consistency between each discriminative output from decoder layers by minimizing the divergence. If we assume that each decoder layer is equivalent to PDE function parameterized by weight parameter $\theta$: $Decoder_i(x;\theta_i) \equiv PDE(x;\theta_i)$ Then our objective is trying to make each discriminative output similar to each other: $PDE(x; \theta_d) \sim PDE(x; \theta_i);\text{ } 0 \leq i < d$ Hence the objective is to $\text{minimize} \sum_{i=0}^{d} D_{KL}(\hat{y} || Decoder_i)$.

OCTAve: 2D en face Optical Coherence Tomography Angiography Vessel Segmentation in Weakly-Supervised Learning with Locality Augmentation

Channel-wise Cross Attention

Channel-wise Cross Attention is a module for semantic segmentation used in the UCTransNet architecture. It is used to fuse features of inconsistent semantics between the Channel Transformer and U-Net decoder. It guides the channel and information filtration of the Transformer features and eliminates the ambiguity with the decoder features. Mathematically, we take the $i$-th level Transformer output $\mathbf{O\_{i}} \in \mathbb{R}^{C×H×W}$ and i-th level decoder feature map $\mathbf{D\_{i}} \in \mathbb{R}^{C×H×W}$ as the inputs of Channel-wise Cross Attention. Spatial squeeze is performed by a global average pooling (GAP) layer, producing vector $\mathcal{G}\left(\mathbf{X}\right) \in \mathbb{R}^{C×1×1}$ with its $k$th channel $\mathcal{G}\left(\mathbf{X}\right) = \frac{1}{H×W}\sum^{H}\_{i=1}\sum^{W}\_{j=1}\mathbf{X}^{k}\left(i, j\right)$. We use this operation to embed the global spatial information and then generate the attention mask: $$ \mathbf{M}\_{i} = \mathbf{L}\_{1} \cdot \mathcal{G}\left(\mathbf{O\_{i}}\right) + \mathbf{L}\_{2} \cdot \mathcal{G}\left(\mathbf{D}\_{i}\right) $$ where $\mathbf{L}\_{1} \in \mathbb{R}^{C×C}$ and $\mathbf{L}\_{2} \in \mathbb{R}^{C×C}$ and being weights of two Linear layers and the ReLU operator $\delta\left(\cdot\right)$. This operation in the equation above encodes the channel-wise dependencies. Following ECA-Net which empirically showed avoiding dimensionality reduction is important for learning channel attention, the authors use a single Linear layer and sigmoid function to build the channel attention map. The resultant vector is used to recalibrate or excite $\mathbf{O\_{i}}$ to $\mathbf{\bar{O}\_{i}} = \sigma\left(\mathbf{M\_{i}}\right) \cdot \mathbf{O\_{i}}$, where the activation $\sigma\left(\mathbf{M\_{i}}\right)$ indicates the importance of each channel. Finally, the masked $\mathbf{\bar{O}}\_{i}$ is concatenated with the up-sampled features of the $i$-th level decoder.

UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer

HyperDenseNet

Recently, dense connections have attracted substantial attention in computer vision because they facilitate gradient flow and implicit deep supervision during training. Particularly, DenseNet that connects each layer to every other layer in a feed-forward fashion and has shown impressive performances in natural image classification tasks. We propose HyperDenseNet, a 3-D fully convolutional neural network that extends the definition of dense connectivity to multi-modal segmentation problems. Each imaging modality has a path, and dense connections occur not only between the pairs of layers within the same path but also between those across different paths. This contrasts with the existing multi-modal CNN approaches, in which modeling several modalities relies entirely on a single joint layer (or level of abstraction) for fusion, typically either at the input or at the output of the network. Therefore, the proposed network has total freedom to learn more complex combinations between the modalities, within and in-between all the levels of abstraction, which increases significantly the learning representation. We report extensive evaluations over two different and highly competitive multi-modal brain tissue segmentation challenges, iSEG 2017 and MRBrainS 2013, with the former focusing on six month infant data and the latter on adult images. HyperDenseNet yielded significant improvements over many state-of-the-art segmentation networks, ranking at the top on both benchmarks. We further provide a comprehensive experimental analysis of features re-use, which confirms the importance of hyper-dense connections in multi-modal representation learning.

HyperDense-Net: A hyper-densely connected CNN for multi-modal image segmentation

PolarMask

PolarMask is an anchor-box free and single-shot instance segmentation method. Specifically, PolarMask takes an image as input and predicts the distance from a sampled positive location (ie a candidate object's center) with respect to the object's contour at each angle, and then assembles the predicted points to produce the final mask. There are several benefits to the system: (1) The polar representation unifies instance segmentation (masks) and object detection (bounding boxes) into a single framework (2) Two modules are designed (i.e. soft polar centerness and polar IoU loss) to sample high-quality center examples and optimize polar contour regression, making the performance of PolarMask does not depend on the bounding box prediction results and more efficient in training. (3) PolarMask is fully convolutional and can be embedded into most off-the-shelf detection methods.

PolarMask++: Enhanced Polar Representation for Single-Shot Instance Segmentation and Beyond

ACNN block

Atrous Convolution Neural Network (ACNN), as a pooling-free network structure, is proposed to achieve full-resolution feature processing using a theoretically optimal dilation setting for a larger receptive field, even with fewer parameters. Compared to other techniques, it can achieve higher segmentation Intersection over Union (IoU) and much less trainable parameters and model sizes, indicating the benefit of full-resolution feature maps in feature processing.

ACNN: a Full Resolution DCNN for Medical Image Segmentation

SIFA

Synergistic Image and Feature Alignment is an unsupervised domain adaptation framework that conducts synergistic alignment of domains from both image and feature perspectives. In SIFA, we simultaneously transform the appearance of images across domains and enhance domain-invariance of the extracted features by leveraging adversarial learning in multiple aspects and with a deeply supervised mechanism. The feature encoder is shared between both adaptive perspectives to leverage their mutual benefits via end-to-end learning.

Unsupervised Bidirectional Cross-Modality Adaptation via Deeply Synergistic Image and Feature Alignment for Medical Image Segmentation

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