A Deep Learning-based in silico Framework for Optimization on Retinal Prosthetic Stimulation

We propose a neural network-based framework to optimize the perceptions simulated by the in silico retinal implant model pulse2percept. The overall pipeline consists of a trainable encoder, a pre-trained retinal implant model and a pre-trained evaluator. The encoder is a U-Net, which takes the original image and outputs the stimulus. The pre-trained retinal implant model is also a U-Net, which is trained to mimic the biomimetic perceptual model implemented in pulse2percept. The evaluator is a shallow VGG classifier, which is trained with original images. Based on 10,000 test images from the MNIST dataset, we show that the convolutional neural network-based encoder performs significantly better than the trivial downsampling approach, yielding a boost in the weighted F1-Score by 36.17% in the pre-trained classifier with 6x10 electrodes. With this fully neural network-based encoder, the quality of the downstream perceptions can be fine-tuned using gradient descent in an end-to-end fashion.

Enhancing Medical Image Segmentation with TransCeption: A Multi-Scale Feature Fusion Approach

While CNN-based methods have been the cornerstone of medical image segmentation due to their promising performance and robustness, they suffer from limitations in capturing long-range dependencies. Transformer-based approaches are currently prevailing since they enlarge the reception field to model global contextual correlation. To further extract rich representations, some extensions of the U-Net employ multi-scale feature extraction and fusion modules and obtain improved performance. Inspired by this idea, we propose TransCeption for medical image segmentation, a pure transformer-based U-shape network featured by incorporating the inception-like module into the encoder and adopting a contextual bridge for better feature fusion. The design proposed in this work is based on three core principles: (1) The patch merging module in the encoder is redesigned with ResInception Patch Merging (RIPM). Multi-branch transformer (MB transformer) adopts the same number of branches as the outputs of RIPM. Combining the two modules enables the model to capture a multi-scale representation within a single stage. (2) We construct an Intra-stage Feature Fusion (IFF) module following the MB transformer to enhance the aggregation of feature maps from all the branches and particularly focus on the interaction between the different channels of all the scales. (3) In contrast to a bridge that only contains token-wise self-attention, we propose a Dual Transformer Bridge that also includes channel-wise self-attention to exploit correlations between scales at different stages from a dual perspective. Extensive experiments on multi-organ and skin lesion segmentation tasks present the superior performance of TransCeption compared to previous work. The code is publicly available at \url{https://github.com/mindflow-institue/TransCeption}.

Advances in Medical Image Analysis with Vision Transformers: A Comprehensive Review

The remarkable performance of the Transformer architecture in natural language processing has recently also triggered broad interest in Computer Vision. Among other merits, Transformers are witnessed as capable of learning long-range dependencies and spatial correlations, which is a clear advantage over convolutional neural networks (CNNs), which have been the de facto standard in Computer Vision problems so far. Thus, Transformers have become an integral part of modern medical image analysis. In this review, we provide an encyclopedic review of the applications of Transformers in medical imaging. Specifically, we present a systematic and thorough review of relevant recent Transformer literature for different medical image analysis tasks, including classification, segmentation, detection, registration, synthesis, and clinical report generation. For each of these applications, we investigate the novelty, strengths and weaknesses of the different proposed strategies and develop taxonomies highlighting key properties and contributions. Further, if applicable, we outline current benchmarks on different datasets. Finally, we summarize key challenges and discuss different future research directions. In addition, we have provided cited papers with their corresponding implementations in https://github.com/mindflow-institue/Awesome-Transformer.

DAE-Former: Dual Attention-guided Efficient Transformer for Medical Image Segmentation

Transformers have recently gained attention in the computer vision domain due to their ability to model long-range dependencies. However, the self-attention mechanism, which is the core part of the Transformer model, usually suffers from quadratic computational complexity with respect to the number of tokens. Many architectures attempt to reduce model complexity by limiting the self-attention mechanism to local regions or by redesigning the tokenization process. In this paper, we propose DAE-Former, a novel method that seeks to provide an alternative perspective by efficiently designing the self-attention mechanism. More specifically, we reformulate the self-attention mechanism to capture both spatial and channel relations across the whole feature dimension while staying computationally efficient. Furthermore, we redesign the skip connection path by including the cross-attention module to ensure the feature reusability and enhance the localization power. Our method outperforms state-of-the-art methods on multi-organ cardiac and skin lesion segmentation datasets without requiring pre-training weights. The code is publicly available at https://github.com/mindflow-institue/DAEFormer.

Medical Image Segmentation Review: The success of U-Net

Automatic medical image segmentation is a crucial topic in the medical domain and successively a critical counterpart in the computer-aided diagnosis paradigm. U-Net is the most widespread image segmentation architecture due to its flexibility, optimized modular design, and success in all medical image modalities. Over the years, the U-Net model achieved tremendous attention from academic and industrial researchers. Several extensions of this network have been proposed to address the scale and complexity created by medical tasks. Addressing the deficiency of the naive U-Net model is the foremost step for vendors to utilize the proper U-Net variant model for their business. Having a compendium of different variants in one place makes it easier for builders to identify the relevant research. Also, for ML researchers it will help them understand the challenges of the biological tasks that challenge the model. To address this, we discuss the practical aspects of the U-Net model and suggest a taxonomy to categorize each network variant. Moreover, to measure the performance of these strategies in a clinical application, we propose fair evaluations of some unique and famous designs on well-known datasets. We provide a comprehensive implementation library with trained models for future research. In addition, for ease of future studies, we created an online list of U-Net papers with their possible official implementation. All information is gathered in https://github.com/NITR098/Awesome-U-Net repository.

Diffusion Models for Medical Image Analysis: A Comprehensive Survey

Denoising diffusion models, a class of generative models, have garnered immense interest lately in various deep-learning problems. A diffusion probabilistic model defines a forward diffusion stage where the input data is gradually perturbed over several steps by adding Gaussian noise and then learns to reverse the diffusion process to retrieve the desired noise-free data from noisy data samples. Diffusion models are widely appreciated for their strong mode coverage and quality of the generated samples despite their known computational burdens. Capitalizing on the advances in computer vision, the field of medical imaging has also observed a growing interest in diffusion models. To help the researcher navigate this profusion, this survey intends to provide a comprehensive overview of diffusion models in the discipline of medical image analysis. Specifically, we introduce the solid theoretical foundation and fundamental concepts behind diffusion models and the three generic diffusion modelling frameworks: diffusion probabilistic models, noise-conditioned score networks, and stochastic differential equations. Then, we provide a systematic taxonomy of diffusion models in the medical domain and propose a multi-perspective categorization based on their application, imaging modality, organ of interest, and algorithms. To this end, we cover extensive applications of diffusion models in the medical domain. Furthermore, we emphasize the practical use case of some selected approaches, and then we discuss the limitations of the diffusion models in the medical domain and propose several directions to fulfill the demands of this field. Finally, we gather the overviewed studies with their available open-source implementations at https://github.com/amirhossein-kz/Awesome-Diffusion-Models-in-Medical-Imaging.

Attention Swin U-Net: Cross-Contextual Attention Mechanism for Skin Lesion Segmentation

Melanoma is caused by the abnormal growth of melanocytes in human skin. Like other cancers, this life-threatening skin cancer can be treated with early diagnosis. To support a diagnosis by automatic skin lesion segmentation, several Fully Convolutional Network (FCN) approaches, specifically the U-Net architecture, have been proposed. The U-Net model with a symmetrical architecture has exhibited superior performance in the segmentation task. However, the locality restriction of the convolutional operation incorporated in the U-Net architecture limits its performance in capturing long-range dependency, which is crucial for the segmentation task in medical images. To address this limitation, recently a Transformer based U-Net architecture that replaces the CNN blocks with the Swin Transformer module has been proposed to capture both local and global representation. In this paper, we propose Att-SwinU-Net, an attention-based Swin U-Net extension, for medical image segmentation. In our design, we seek to enhance the feature re-usability of the network by carefully designing the skip connection path. We argue that the classical concatenation operation utilized in the skip connection path can be further improved by incorporating an attention mechanism. By performing a comprehensive ablation study on several skin lesion segmentation datasets, we demonstrate the effectiveness of our proposed attention mechanism.

Instance Segmentation of Dense and Overlapping Objects via Layering

Instance segmentation aims to delineate each individual object of interest in an image. State-of-the-art approaches achieve this goal by either partitioning semantic segmentations or refining coarse representations of detected objects. In this work, we propose a novel approach to solve the problem via object layering, i.e. by distributing crowded, even overlapping objects into different layers. By grouping spatially separated objects in the same layer, instances can be effortlessly isolated by extracting connected components in each layer. In comparison to previous methods, our approach is not affected by complex object shapes or object overlaps. With minimal post-processing, our method yields very competitive results on a diverse line of datasets: C. elegans (BBBC), Overlapping Cervical Cells (OCC) and cultured neuroblastoma cells (CCDB). The source code is publicly available.

TransDeepLab: Convolution-Free Transformer-based DeepLab v3+ for Medical Image Segmentation

Convolutional neural networks (CNNs) have been the de facto standard in a diverse set of computer vision tasks for many years. Especially, deep neural networks based on seminal architectures such as U-shaped models with skip-connections or atrous convolution with pyramid pooling have been tailored to a wide range of medical image analysis tasks. The main advantage of such architectures is that they are prone to detaining versatile local features. However, as a general consensus, CNNs fail to capture long-range dependencies and spatial correlations due to the intrinsic property of confined receptive field size of convolution operations. Alternatively, Transformer, profiting from global information modelling that stems from the self-attention mechanism, has recently attained remarkable performance in natural language processing and computer vision. Nevertheless, previous studies prove that both local and global features are critical for a deep model in dense prediction, such as segmenting complicated structures with disparate shapes and configurations. To this end, this paper proposes TransDeepLab, a novel DeepLab-like pure Transformer for medical image segmentation. Specifically, we exploit hierarchical Swin-Transformer with shifted windows to extend the DeepLabv3 and model the Atrous Spatial Pyramid Pooling (ASPP) module. A thorough search of the relevant literature yielded that we are the first to model the seminal DeepLab model with a pure Transformer-based model. Extensive experiments on various medical image segmentation tasks verify that our approach performs superior or on par with most contemporary works on an amalgamation of Vision Transformer and CNN-based methods, along with a significant reduction of model complexity. The codes and trained models are publicly available at https://github.com/rezazad68/transdeeplab

TransNorm: Transformer Provides a Strong Spatial Normalization Mechanism for a Deep Segmentation Model

In the past few years, convolutional neural networks (CNNs), particularly U-Net, have been the prevailing technique in the medical image processing era. Specifically, the seminal U-Net, as well as its alternatives, have successfully managed to address a wide variety of medical image segmentation tasks. However, these architectures are intrinsically imperfect as they fail to exhibit long-range interactions and spatial dependencies leading to a severe performance drop in the segmentation of medical images with variable shapes and structures. Transformers, preliminary proposed for sequence-to-sequence prediction, have arisen as surrogate architectures to precisely model global information assisted by the self-attention mechanism. Despite being feasibly designed, utilizing a pure Transformer for image segmentation purposes can result in limited localization capacity stemming from inadequate low-level features. Thus, a line of research strives to design robust variants of Transformer-based U-Net. In this paper, we propose Trans-Norm, a novel deep segmentation framework which concomitantly consolidates a Transformer module into both encoder and skip-connections of the standard U-Net. We argue that the expedient design of skip-connections can be crucial for accurate segmentation as it can assist in feature fusion between the expanding and contracting paths. In this respect, we derive a Spatial Normalization mechanism from the Transformer module to adaptively recalibrate the skip connection path. Extensive experiments across three typical tasks for medical image segmentation demonstrate the effectiveness of TransNorm. The codes and trained models are publicly available at https://github.com/rezazad68/transnorm.