KiU-Net: Towards Accurate Segmentation of Biomedical Images Using Over-Complete Representations

GU-Net: Causal relationship-based generative medical image segmentation model

Due to significant anatomical variations in medical images across different cases, medical image segmentation is a highly challenging task. Convolutional neural networks have shown faster and more accurate performance in medical image segmentation. However, existing networks for medical image segmentation mostly rely on independent training of the model using data samples and loss functions, lacking interactive training and feedback mechanisms. This leads to a relatively singular training approach for the models, and furthermore, some networks can only perform segmentation for specific diseases. In this paper, we propose a causal relationship-based generative medical image segmentation model named GU-Net. We integrate a counterfactual attention mechanism combined with CBAM into the decoder of U-Net as a generative network, and then combine it with a GAN network where the discriminator is used for backpropagation. This enables alternate optimization and training between the generative network and discriminator, enhancing the expressive and learning capabilities of the network model to output prediction segmentation results closer to the ground truth. Additionally, the interaction and transmission of information help the network model capture richer feature representations, extract more accurate features, reduce overfitting, and improve model stability and robustness through feedback mechanisms. Experimental results demonstrate that our proposed GU-Net network achieves better segmentation performance not only in cases with abundant data samples and relatively simple segmentation targets or high contrast between the target and background regions but also in scenarios with limited data samples and challenging segmentation tasks. Comparing with existing U-Net networks with attention mechanisms, GU-Net consistently improves Dice scores by 1.19%, 2.93%, 5.01%, and 5.50% on ISIC 2016, ISIC 2017, ISIC 2018, and Gland Segmentation datasets, respectively.

EAAC-Net: An Efficient Adaptive Attention and Convolution Fusion Network for Skin Lesion Segmentation

Accurate segmentation of skin lesions in dermoscopic images is of key importance for quantitative analysis of melanoma. Although existing medical image segmentation methods significantly improve skin lesion segmentation, they still have limitations in extracting local features with global information, do not handle challenging lesions well, and usually have a large number of parameters and high computational complexity. To address these issues, this paper proposes an efficient adaptive attention and convolutional fusion network for skin lesion segmentation (EAAC-Net). We designed two parallel encoders, where the efficient adaptive attention feature extraction module (EAAM) adaptively establishes global spatial dependence and global channel dependence by constructing the adjacency matrix of the directed graph and can adaptively filter out the least relevant tokens at the coarse-grained region level, thus reducing the computational complexity of the self-attention mechanism. The efficient multiscale attention-based convolution module (EMA⋅C) utilizes multiscale attention for cross-space learning of local features extracted from the convolutional layer to enhance the representation of richly detailed local features. In addition, we designed a reverse attention feature fusion module (RAFM) to enhance the effective boundary information gradually. To validate the performance of our proposed network, we compared it with other methods on ISIC 2016, ISIC 2018, and PH2 public datasets, and the experimental results show that EAAC-Net has superior segmentation performance under commonly used evaluation metrics.

Automatic Segmentation and Alignment of Uterine Shapes from 3D Ultrasound Data

BACKGROUND

The uterus is the most important organ in the female reproductive system. Its shape plays a critical role in fertility and pregnancy outcomes. Advances in medical imaging, such as 3D ultrasound, have significantly improved the exploration of the female genital tract, thereby enhancing gynecological healthcare. Despite well-documented data for organs like the liver and heart, large-scale studies on the uterus are lacking. Existing classifications, such as VCUAM and ESHRE/ESGE, provide different definitions for normal uterine shapes but are not based on real-world measurements. Moreover, the lack of comprehensive datasets significantly hinders research in this area. Our research, part of the larger NURSE study, aims to fill this gap by establishing the shape of a normal uterus using real-world 3D vaginal ultrasound scans. This will facilitate research into uterine shape abnormalities associated with infertility and recurrent miscarriages.

METHODS

We developed an automated system for the segmentation and alignment of uterine shapes from 3D ultrasound data, which consists of two steps: automatic segmentation of the uteri in 3D ultrasound scans using deep learning techniques, and alignment of the resulting shapes with standard geometrical approaches, enabling the extraction of the normal shape for future analysis. The system was trained and validated on a comprehensive dataset of 3D ultrasound images from multiple medical centers. Its performance was evaluated by comparing the automated results with manual annotations provided by expert clinicians.

RESULTS

The presented approach demonstrated high accuracy in segmenting and aligning uterine shapes from 3D ultrasound data. The segmentation achieved an average Dice similarity coefficient (DSC) of 0.90. Our method for aligning uterine shapes showed minimal translation and rotation errors compared to traditional methods, with the preliminary average shape exhibiting characteristics consistent with expert findings of a normal uterus.

CONCLUSION

We have presented an approach to automatically segment and align uterine shapes from 3D ultrasound data. We trained a deep learning nnU-Net model that achieved high accuracy and proposed an alignment method using a combination of standard geometrical techniques. Additionally, we have created a publicly available dataset of 3D transvaginal ultrasound volumes with manual annotations of uterine cavities to support further research and development in this field. The dataset and the trained models are available at https://github.com/UL-FRI-LGM/UterUS.

Boundary guidance network for medical image segmentation

Accurate segmentation of the tumor area is crucial for the treatment and prognosis of patients with bladder cancer. Cystoscopy is the gold standard for diagnosing bladder tumors. However, The vast majority of current work uses deep learning to identify and segment tumors from CT and MRI findings, and rarely involves cystoscopy findings. Accurately segmenting bladder tumors remains a great challenge due to their diverse morphology and fuzzy boundaries. In order to solve the above problems, this paper proposes a medical image segmentation network with boundary guidance called boundary guidance network. This network combines local features extracted by CNNs and long-range dependencies between different levels inscribed by Parallel ViT, which can capture tumor features more effectively. The Boundary extracted module is designed to extract boundary features and utilize the boundary features to guide the decoding process. Foreground-background dual-channel decoding is performed by boundary integrated module. Experimental results on our proposed new cystoscopic bladder tumor dataset (BTD) show that our method can efficiently perform accurate segmentation of tumors and retain more boundary information, achieving an IoU score of 91.3%, a Hausdorff Distance of 10.43, an mAP score of 85.3%, and a F1 score of 94.8%. On BTD and three other public datasets, our model achieves the best scores compared to state-of-the-art methods, which proves the effectiveness of our model for common medical image segmentation.

Shape-Scale Co-Awareness Network for 3D Brain Tumor Segmentation

The accurate segmentation of brain tumor is significant in clinical practice. Convolutional Neural Network (CNN)-based methods have made great progress in brain tumor segmentation due to powerful local modeling ability. However, brain tumors are frequently pattern-agnostic, i.e. variable in shape, size and location, which can not be effectively matched by traditional CNN-based methods with local and regular receptive fields. To address the above issues, we propose a shape-scale co-awareness network (S2CA-Net) for brain tumor segmentation, which can efficiently learn shape-aware and scale-aware features simultaneously to enhance pattern-agnostic representations. Primarily, three key components are proposed to accomplish the co-awareness of shape and scale. The Local-Global Scale Mixer (LGSM) decouples the extraction of local and global context by adopting the CNN-Former parallel structure, which contributes to obtaining finer hierarchical features. The Multi-level Context Aggregator (MCA) enriches the scale diversity of input patches by modeling global features across multiple receptive fields. The Multi-Scale Attentive Deformable Convolution (MS-ADC) learns the target deformation based on the multiscale inputs, which motivates the network to enforce feature constraints both in terms of scale and shape for optimal feature matching. Overall, LGSM and MCA focus on enhancing the scale-awareness of the network to cope with the size and location variations, while MS-ADC focuses on capturing deformation information for optimal shape matching. Finally, their effective integration prompts the network to perceive variations in shape and scale simultaneously, which can robustly tackle the variations in patterns of brain tumors. The experimental results on BraTS 2019, BraTS 2020, MSD BTS Task and BraTS2023-MEN show that S2CA-Net has superior overall performance in accuracy and efficiency compared to other state-of-the-art methods. Code: https://github.com/jiangyu945/S2CA-Net.

Improving abdominal image segmentation with overcomplete shape priors

The extraction of abdominal structures using deep learning has recently experienced a widespread interest in medical image analysis. Automatic abdominal organ and vessel segmentation is highly desirable to guide clinicians in computer-assisted diagnosis, therapy, or surgical planning. Despite a good ability to extract large organs, the capacity of U-Net inspired architectures to automatically delineate smaller structures remains a major issue, especially given the increase in receptive field size as we go deeper into the network. To deal with various abdominal structure sizes while exploiting efficient geometric constraints, we present a novel approach that integrates into deep segmentation shape priors from a semi-overcomplete convolutional auto-encoder (S-OCAE) embedding. Compared to standard convolutional auto-encoders (CAE), it exploits an over-complete branch that projects data onto higher dimensions to better characterize anatomical structures with a small spatial extent. Experiments on abdominal organs and vessel delineation performed on various publicly available datasets highlight the effectiveness of our method compared to state-of-the-art, including U-Net trained without and with shape priors from a traditional CAE. Exploiting a semi-overcomplete convolutional auto-encoder embedding as shape priors improves the ability of deep segmentation models to provide realistic and accurate abdominal structure contours.

SwinPA-Net: Swin Transformer-Based Multiscale Feature Pyramid Aggregation Network for Medical Image Segmentation

The precise segmentation of medical images is one of the key challenges in pathology research and clinical practice. However, many medical image segmentation tasks have problems such as large differences between different types of lesions and similar shapes as well as colors between lesions and surrounding tissues, which seriously affects the improvement of segmentation accuracy. In this article, a novel method called Swin Pyramid Aggregation network (SwinPA-Net) is proposed by combining two designed modules with Swin Transformer to learn more powerful and robust features. The two modules, named dense multiplicative connection (DMC) module and local pyramid attention (LPA) module, are proposed to aggregate the multiscale context information of medical images. The DMC module cascades the multiscale semantic feature information through dense multiplicative feature fusion, which minimizes the interference of shallow background noise to improve the feature expression and solves the problem of excessive variation in lesion size and type. Moreover, the LPA module guides the network to focus on the region of interest by merging the global attention and the local attention, which helps to solve similar problems. The proposed network is evaluated on two public benchmark datasets for polyp segmentation task and skin lesion segmentation task as well as a clinical private dataset for laparoscopic image segmentation task. Compared with existing state-of-the-art (SOTA) methods, the SwinPA-Net achieves the most advanced performance and can outperform the second-best method on the mean Dice score by 1.68%, 0.8%, and 1.2% on the three tasks, respectively.

Semi-automatic fine delineation scheme for pancreatic cancer

BACKGROUND

Pancreatic cancer fine delineation in medical images by physicians is a major challenge due to the vast volume of medical images and the variability of patients.

PURPOSE

A semi-automatic fine delineation scheme was designed to assist doctors in accurately and quickly delineating the cancer target region to improve the delineation accuracy of pancreatic cancer in computed tomography (CT) images and effectively reduce the workload of doctors.

METHODS

A target delineation scheme in image blocks was also designed to provide more information for the deep learning delineation model. The start and end slices of the image block were manually delineated by physicians, and the cancer in the middle slices were accurately segmented using a three-dimensional Res U-Net model. Specifically, the input of the network is the CT image of the image block and the delineation of the cancer in the start and end slices, while the output of the network is the cancer area in the middle slices of the image block. Meanwhile, the model performance of pancreatic cancer delineation and the workload of doctors in different image block sizes were studied.

RESULTS

We used 37 3D CT volumes for training, 11 volumes for validating and 11 volumes for testing. The influence of different image block sizes on doctors' workload was compared quantitatively. Experimental results showed that the physician's workload was minimal when the image block size was 5, and all cancer could be accurately delineated. The Dice similarity coefficient was 0.894 ± 0.029, the 95% Hausdorff distance was 3.465 ± 0.710 mm, the normalized surface Dice was 0.969 ± 0.019. By completing the accurate delineation of all the CT images, the speed of the new method is 2.16 times faster than that of manual sketching.

CONCLUSION

Our proposed 3D semi-automatic delineative method based on the idea of block prediction could accurately delineate CT images of pancreatic cancer and effectively deal with the challenges of class imbalance, background distractions, and non-rigid geometrical features. This study had a significant advantage in reducing doctors' workload, and was expected to help doctors improve their work efficiency in clinical application.

SADSNet: A robust 3D synchronous segmentation network for liver and liver tumors based on spatial attention mechanism and deep supervision

Highlights

• Introduce a data augmentation strategy to expand the required different morphological data during the training and learning phase, and improve the algorithm's feature learning ability for complex and diverse tumor morphology CT images.• Design attention mechanisms for encoding and decoding paths to extract fine pixel level features, improve feature extraction capabilities, and achieve efficient spatial channel feature fusion.• The deep supervision layer is used to correct and decode the final image data to provide high accuracy of results.• The effectiveness of this method has been affirmed through validation on the LITS, 3DIRCADb, and SLIVER datasets.

BACKGROUND

Accurately extracting liver and liver tumors from medical images is an important step in lesion localization and diagnosis, surgical planning, and postoperative monitoring. However, the limited number of radiation therapists and a great number of images make this work time-consuming.

OBJECTIVE

This study designs a spatial attention deep supervised network (SADSNet) for simultaneous automatic segmentation of liver and tumors.

METHOD

Firstly, self-designed spatial attention modules are introduced at each layer of the encoder and decoder to extract image features at different scales and resolutions, helping the model better capture liver tumors and fine structures. The designed spatial attention module is implemented through two gate signals related to liver and tumors, as well as changing the size of convolutional kernels; Secondly, deep supervision is added behind the three layers of the decoder to assist the backbone network in feature learning and improve gradient propagation, enhancing robustness.

RESULTS

The method was testing on LITS, 3DIRCADb, and SLIVER datasets. For the liver, it obtained dice similarity coefficients of 97.03%, 96.11%, and 97.40%, surface dice of 81.98%, 82.53%, and 86.29%, 95% hausdorff distances of 8.96 mm, 8.26 mm, and 3.79 mm, and average surface distances of 1.54 mm, 1.19 mm, and 0.81 mm. Additionally, it also achieved precise tumor segmentation, which with dice scores of 87.81% and 87.50%, surface dice of 89.63% and 84.26%, 95% hausdorff distance of 12.96 mm and 16.55 mm, and average surface distances of 1.11 mm and 3.04 mm on LITS and 3DIRCADb, respectively.

CONCLUSION

The experimental results show that the proposed method is effective and superior to some other methods. Therefore, this method can provide technical support for liver and liver tumor segmentation in clinical practice.

A Novel Deep Learning Model for Medical Image Segmentation with Convolutional Neural Network and Transformer

Accurate segmentation of medical images is essential for clinical decision-making, and deep learning techniques have shown remarkable results in this area. However, existing segmentation models that combine transformer and convolutional neural networks often use skip connections in U-shaped networks, which may limit their ability to capture contextual information in medical images. To address this limitation, we propose a coordinated mobile and residual transformer UNet (MRC-TransUNet) that combines the strengths of transformer and UNet architectures. Our approach uses a lightweight MR-ViT to address the semantic gap and a reciprocal attention module to compensate for the potential loss of details. To better explore long-range contextual information, we use skip connections only in the first layer and add MR-ViT and RPA modules in the subsequent downsampling layers. In our study, we evaluated the effectiveness of our proposed method on three different medical image segmentation datasets, namely, breast, brain, and lung. Our proposed method outperformed state-of-the-art methods in terms of various evaluation metrics, including the Dice coefficient and Hausdorff distance. These results demonstrate that our proposed method can significantly improve the accuracy of medical image segmentation and has the potential for clinical applications. Illustration of the proposed MRC-TransUNet. For the input medical images, we first subject them to an intrinsic downsampling operation and then replace the original jump connection structure using MR-ViT. The output feature representations at different scales are fused by the RPA module. Finally, an upsampling operation is performed to fuse the features to restore them to the same resolution as the input image.

Optimization of U-shaped pure transformer medical image segmentation network

In recent years, neural networks have made pioneering achievements in the field of medical imaging. In particular, deep neural networks based on U-shaped structures are widely used in different medical image segmentation tasks. In order to improve the early diagnosis and clinical decision-making system of lung diseases, it has become a key step to use the neural network for lung segmentation to assist in positioning and observing the shape. There is still the problem of low precision. For the sake of achieving better segmentation accuracy, an optimized pure Transformer U-shaped segmentation is proposed in this article. The optimization segmentation network adopts the method of adding skip connections and performing special splicing processing, which reduces the information loss in the encoding process and increases the information in the decoding process, so as to achieve the purpose of improving the segmentation accuracy. The final experiment shows that our improved network achieves 97.86% accuracy in segmentation of the "Chest Xray Masks and Labels" dataset, which is better than the full convolutional network or the combination of Transformer and convolution.

DRU-Net: Pulmonary Artery Segmentation via Dense Residual U-Network with Hybrid Loss Function

The structure and topology of the pulmonary arteries is crucial to understand, plan, and conduct medical treatment in the thorax area. Due to the complex anatomy of the pulmonary vessels, it is not easy to distinguish between the arteries and veins. The pulmonary arteries have a complex structure with an irregular shape and adjacent tissues, which makes automatic segmentation a challenging task. A deep neural network is required to segment the topological structure of the pulmonary artery. Therefore, in this study, a Dense Residual U-Net with a hybrid loss function is proposed. The network is trained on augmented Computed Tomography volumes to improve the performance of the network and prevent overfitting. Moreover, the hybrid loss function is implemented to improve the performance of the network. The results show an improvement in the Dice and HD95 scores over state-of-the-art techniques. The average scores achieved for the Dice and HD95 scores are 0.8775 and 4.2624 mm, respectively. The proposed method will support physicians in the challenging task of preoperative planning of thoracic surgery, where the correct assessment of the arteries is crucial.

FM-Unet: Biomedical image segmentation based on feedback mechanism Unet

With the development of deep learning, medical image segmentation technology has made significant progress in the field of computer vision. The Unet is a pioneering work, and many researchers have conducted further research based on this architecture. However, we found that most of these architectures are improvements in the backward propagation and integration of the network, and few changes are made to the forward propagation and information integration of the network. Therefore, we propose a feedback mechanism Unet (FM-Unet) model, which adds feedback paths to the encoder and decoder paths of the network, respectively, to help the network fuse the information of the next step in the current encoder and decoder. The problem of encoder information loss and decoder information shortage can be well solved. The proposed model has more moderate network parameters, and the simultaneous multi-node information fusion can alleviate the gradient disappearance. We have conducted experiments on two public datasets, and the results show that FM-Unet achieves satisfactory results.

Polarization-Dependent Metasurface Enables Near-Infrared Dual-Modal Single-Pixel Sensing

Infrared single-pixel sensing with the two most representative modes, bright-field imaging and edge-enhanced imaging, has great application potential in biomedical diagnosis and defect inspection. Building a multifunctional and miniature optical computing device for infrared single-pixel sensing is extremely intriguing. Here, we propose and validate a dual-modal device based on a well-designed metasurface, which enables near-infrared bright-field and edge-enhanced single-pixel imaging. By changing the polarization of the incident beam, these two different modes can be switched. Simulations validate that our device can achieve high-fidelity dual-modal single-pixel sensing at 0.9 μm with certain noise robustness. We also investigate the generalization of our metasurface-based device and validate that different illumination patterns are applied to our device. Moreover, these output images by our device can be efficiently utilized for biomedical image segmentation. We envision this novel device may open a vista in dual-modal infrared single-pixel sensing.

3D Shuffle-Mixer: An Efficient Context-Aware Vision Learner of Transformer-MLP Paradigm for Dense Prediction in Medical Volume

Dense prediction in medical volume provides enriched guidance for clinical analysis. CNN backbones have met bottleneck due to lack of long-range dependencies and global context modeling power. Recent works proposed to combine vision transformer with CNN, due to its strong global capture ability and learning capability. However, most works are limited to simply applying pure transformer with several fatal flaws (i.e., lack of inductive bias, heavy computation and little consideration for 3D data). Therefore, designing an elegant and efficient vision transformer learner for dense prediction in medical volume is promising and challenging. In this paper, we propose a novel 3D Shuffle-Mixer network of a new Local Vision Transformer-MLP paradigm for medical dense prediction. In our network, a local vision transformer block is utilized to shuffle and learn spatial context from full-view slices of rearranged volume, a residual axial-MLP is designed to mix and capture remaining volume context in a slice-aware manner, and a MLP view aggregator is employed to project the learned full-view rich context to the volume feature in a view-aware manner. Moreover, an Adaptive Scaled Enhanced Shortcut is proposed for local vision transformer to enhance feature along spatial and channel dimensions adaptively, and a CrossMerge is proposed to skip-connect the multi-scale feature appropriately in the pyramid architecture. Extensive experiments demonstrate the proposed model outperforms other state-of-the-art medical dense prediction methods.

GL-Segnet: Global-Local representation learning net for medical image segmentation

Medical image segmentation has long been a compelling and fundamental problem in the realm of neuroscience. This is an extremely challenging task due to the intensely interfering irrelevant background information to segment the target. State-of-the-art methods fail to consider simultaneously addressing both long-range and short-range dependencies, and commonly emphasize the semantic information characterization capability while ignoring the geometric detail information implied in the shallow feature maps resulting in the dropping of crucial features. To tackle the above problem, we propose a Global-Local representation learning net for medical image segmentation, namely GL-Segnet. In the Feature encoder, we utilize the Multi-Scale Convolution (MSC) and Multi-Scale Pooling (MSP) modules to encode the global semantic representation information at the shallow level of the network, and multi-scale feature fusion operations are applied to enrich local geometric detail information in a cross-level manner. Beyond that, we adopt a global semantic feature extraction module to perform filtering of irrelevant background information. In Attention-enhancing Decoder, we use the Attention-based feature decoding module to refine the multi-scale fused feature information, which provides effective cues for attention decoding. We exploit the structural similarity between images and the edge gradient information to propose a hybrid loss to improve the segmentation accuracy of the model. Extensive experiments on medical image segmentation from Glas, ISIC, Brain Tumors and SIIM-ACR demonstrated that our GL-Segnet is superior to existing state-of-art methods in subjective visual performance and objective evaluation.

Semantic Decomposition Network With Contrastive and Structural Constraints for Dental Plaque Segmentation

Segmenting dental plaque from images of medical reagent staining provides valuable information for diagnosis and the determination of follow-up treatment plan. However, accurate dental plaque segmentation is a challenging task that requires identifying teeth and dental plaque subjected to semantic-blur regions (i.e., confused boundaries in border regions between teeth and dental plaque) and complex variations of instance shapes, which are not fully addressed by existing methods. Therefore, we propose a semantic decomposition network (SDNet) that introduces two single-task branches to separately address the segmentation of teeth and dental plaque and designs additional constraints to learn category-specific features for each branch, thus facilitating the semantic decomposition and improving the performance of dental plaque segmentation. Specifically, SDNet learns two separate segmentation branches for teeth and dental plaque in a divide-and-conquer manner to decouple the entangled relation between them. Each branch that specifies a category tends to yield accurate segmentation. To help these two branches better focus on category-specific features, two constraint modules are further proposed: 1) contrastive constraint module (CCM) to learn discriminative feature representations by maximizing the distance between different category representations, so as to reduce the negative impact of semantic-blur regions on feature extraction; 2) structural constraint module (SCM) to provide complete structural information for dental plaque of various shapes by the supervision of an boundary-aware geometric constraint. Besides, we construct a large-scale open-source Stained Dental Plaque Segmentation dataset (SDPSeg), which provides high-quality annotations for teeth and dental plaque. Experimental results on SDPSeg datasets show SDNet achieves state-of-the-art performance.

Crosslink-Net: Double-Branch Encoder Network via Fusing Vertical and Horizontal Convolutions for Medical Image Segmentation

Accurate image segmentation plays a crucial role in medical image analysis, yet it faces great challenges caused by various shapes, diverse sizes, and blurry boundaries. To address these difficulties, square kernel-based encoder-decoder architectures have been proposed and widely used, but their performance remains unsatisfactory. To further address these challenges, we present a novel double-branch encoder architecture. Our architecture is inspired by two observations. (1) Since the discrimination of the features learned via square convolutional kernels needs to be further improved, we propose utilizing nonsquare vertical and horizontal convolutional kernels in a double-branch encoder so that the features learned by both branches can be expected to complement each other. (2) Considering that spatial attention can help models to better focus on the target region in a large-sized image, we develop an attention loss to further emphasize the segmentation of small-sized targets. With the above two schemes, we develop a novel double-branch encoder-based segmentation framework for medical image segmentation, namely, Crosslink-Net, and validate its effectiveness on five datasets with experiments. The code is released at https://github.com/Qianyu1226/Crosslink-Net.

Open-Source Biomedical Image Analysis Models: A Meta-Analysis and Continuous Survey

Open-source research software has proven indispensable in modern biomedical image analysis. A multitude of open-source platforms drive image analysis pipelines and help disseminate novel analytical approaches and algorithms. Recent advances in machine learning allow for unprecedented improvement in these approaches. However, these novel algorithms come with new requirements in order to remain open source. To understand how these requirements are met, we have collected 50 biomedical image analysis models and performed a meta-analysis of their respective papers, source code, dataset, and trained model parameters. We concluded that while there are many positive trends in openness, only a fraction of all publications makes all necessary elements available to the research community.

KiU-Net: Overcomplete Convolutional Architectures for Biomedical Image and Volumetric Segmentation

Most methods for medical image segmentation use U-Net or its variants as they have been successful in most of the applications. After a detailed analysis of these "traditional" encoder-decoder based approaches, we observed that they perform poorly in detecting smaller structures and are unable to segment boundary regions precisely. This issue can be attributed to the increase in receptive field size as we go deeper into the encoder. The extra focus on learning high level features causes U-Net based approaches to learn less information about low-level features which are crucial for detecting small structures. To overcome this issue, we propose using an overcomplete convolutional architecture where we project the input image into a higher dimension such that we constrain the receptive field from increasing in the deep layers of the network. We design a new architecture for im- age segmentation- KiU-Net which has two branches: (1) an overcomplete convolutional network Kite-Net which learns to capture fine details and accurate edges of the input, and (2) U-Net which learns high level features. Furthermore, we also propose KiU-Net 3D which is a 3D convolutional architecture for volumetric segmentation. We perform a detailed study of KiU-Net by performing experiments on five different datasets covering various image modalities. We achieve a good performance with an additional benefit of fewer parameters and faster convergence. We also demonstrate that the extensions of KiU-Net based on residual blocks and dense blocks result in further performance improvements. Code: https://github.com/jeya-maria-jose/KiU-Net-pytorch.

Over-and-Under Complete Convolutional RNN for MRI Reconstruction

Reconstructing magnetic resonance (MR) images from under-sampled data is a challenging problem due to various artifacts introduced by the under-sampling operation. Recent deep learning-based methods for MR image reconstruction usually leverage a generic auto-encoder architecture which captures low-level features at the initial layers and high-level features at the deeper layers. Such networks focus much on global features which may not be optimal to reconstruct the fully-sampled image. In this paper, we propose an Over-and-Under Complete Convolutional Recurrent Neural Network (OUCR), which consists of an overcomplete and an undercomplete Convolutional Recurrent Neural Network (CRNN). The overcomplete branch gives special attention in learning local structures by restraining the receptive field of the network. Combining it with the undercomplete branch leads to a network which focuses more on low-level features without losing out on the global structures. Extensive experiments on two datasets demonstrate that the proposed method achieves significant improvements over the compressed sensing and popular deep learning-based methods with less number of trainable parameters.

Mass segmentation for whole mammograms via attentive multi-task learning framework

Mass segmentation in the mammogram is a necessary and challenging task in the computer-aided diagnosis of breast cancer. Most of the existing methods tended to segment the mass by manually or automatically extracting mass-centered image patches. However, manual patch extraction is time-consuming, and automatic patch extraction can introduce errors that will affect the performance of subsequent segmentation.In order to improve the efficiency of mass segmentation and reduce segmentation errors, we proposed a novel mass segmentation method based on an attentive multi-task learning network (MTLNet), which is an end-to-end model to accurately segment mass in the whole mammogram directly, without the need for extraction in advance with the center of mass image patch. In MTLNet, we applied group convolution to the feature extraction network, which not only reduced the redundancy of the network but also improved the capacity of feature learning. Secondly, an attention mechanism is added to the backbone to highlight the feature channels that contain rich information. Eventually, the multi-task learning framework is employed in the model, which reduces the risk of model overfitting and enables the model not only to segment the mass but also to classify and locate the mass. We \hl{used five-fold cross validation to evaluate the performance of the proposed method under detection and segmentation tasks respectively on the two public mammographic datasets INbreast and CBIS-DDSM, and our method achieved the Dice index of 0.826 on INbreast and 0.863 on CBIS-DDSM.