arXiv subjects

Dorit Merhof

Publications and source records attributed to Dorit Merhof.

At least 73 records · Page 4Linked to original sources

arXiv2023

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.

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arXiv2023

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}.

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arXiv2023

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation

Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, and quantitative and qualitative results. Our code is publicly available at: https://github.com/amirhossein-kz/HiFormer

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arXiv2022

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.

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arXiv2022

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

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arXiv2022

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.

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arXiv2022

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.

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arXiv2022

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

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arXiv2022

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.

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arXiv2022

Transfer Learning Gaussian Anomaly Detection by Fine-tuning Representations

Current state-of-the-art anomaly detection (AD) methods exploit the powerful representations yielded by large-scale ImageNet training. However, catastrophic forgetting prevents the successful fine-tuning of pre-trained representations on new datasets in the semi-supervised setting, and representations are therefore commonly fixed. In our work, we propose a new method to overcome catastrophic forgetting and thus successfully fine-tune pre-trained representations for AD in the transfer learning setting. Specifically, we induce a multivariate Gaussian distribution for the normal class based on the linkage between generative and discriminative modeling, and use the Mahalanobis distance of normal images to the estimated distribution as training objective. We additionally propose to use augmentations commonly employed for vicinal risk minimization in a validation scheme to detect onset of catastrophic forgetting. Extensive evaluations on the public MVTec dataset reveal that a new state of the art is achieved by our method in the AD task while simultaneously achieving anomaly segmentation performance comparable to prior state of the art. Further, ablation studies demonstrate the importance of the induced Gaussian distribution as well as the robustness of the proposed fine-tuning scheme with respect to the choice of augmentations.

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arXiv2022

Improving Unsupervised Stain-To-Stain Translation using Self-Supervision and Meta-Learning

In digital pathology, many image analysis tasks are challenged by the need for large and time-consuming manual data annotations to cope with various sources of variability in the image domain. Unsupervised domain adaptation based on image-to-image translation is gaining importance in this field by addressing variabilities without the manual overhead. Here, we tackle the variation of different histological stains by unsupervised stain-to-stain translation to enable a stain-independent applicability of a deep learning segmentation model. We use CycleGANs for stain-to-stain translation in kidney histopathology, and propose two novel approaches to improve translational effectivity. First, we integrate a prior segmentation network into the CycleGAN for a self-supervised, application-oriented optimization of translation through semantic guidance, and second, we incorporate extra channels to the translation output to implicitly separate artificial meta-information otherwise encoded for tackling underdetermined reconstructions. The latter showed partially superior performances to the unmodified CycleGAN, but the former performed best in all stains providing instance-level Dice scores ranging between 78% and 92% for most kidney structures, such as glomeruli, tubules, and veins. However, CycleGANs showed only limited performance in the translation of other structures, e.g. arteries. Our study also found somewhat lower performance for all structures in all stains when compared to segmentation in the original stain. Our study suggests that with current unsupervised technologies, it seems unlikely to produce generally applicable simulated stains.

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arXiv2022

Intervertebral Disc Labeling With Learning Shape Information, A Look Once Approach

Accurate and automatic segmentation of intervertebral discs from medical images is a critical task for the assessment of spine-related diseases such as osteoporosis, vertebral fractures, and intervertebral disc herniation. To date, various approaches have been developed in the literature which routinely relies on detecting the discs as the primary step. A disadvantage of many cohort studies is that the localization algorithm also yields false-positive detections. In this study, we aim to alleviate this problem by proposing a novel U-Net-based structure to predict a set of candidates for intervertebral disc locations. In our design, we integrate the image shape information (image gradients) to encourage the model to learn rich and generic geometrical information. This additional signal guides the model to selectively emphasize the contextual representation and suppress the less discriminative features. On the post-processing side, to further decrease the false positive rate, we propose a permutation invariant 'look once' model, which accelerates the candidate recovery procedure. In comparison with previous studies, our proposed approach does not need to perform the selection in an iterative fashion. The proposed method was evaluated on the spine generic public multi-center dataset and demonstrated superior performance compared to previous work. We have provided the implementation code in https://github.com/rezazad68/intervertebral-lookonce

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arXiv2022

SMU-Net: Style matching U-Net for brain tumor segmentation with missing modalities

Gliomas are one of the most prevalent types of primary brain tumours, accounting for more than 30\% of all cases and they develop from the glial stem or progenitor cells. In theory, the majority of brain tumours could well be identified exclusively by the use of Magnetic Resonance Imaging (MRI). Each MRI modality delivers distinct information on the soft tissue of the human brain and integrating all of them would provide comprehensive data for the accurate segmentation of the glioma, which is crucial for the patient's prognosis, diagnosis, and determining the best follow-up treatment. Unfortunately, MRI is prone to artifacts for a variety of reasons, which might result in missing one or more MRI modalities. Various strategies have been proposed over the years to synthesize the missing modality or compensate for the influence it has on automated segmentation models. However, these methods usually fail to model the underlying missing information. In this paper, we propose a style matching U-Net (SMU-Net) for brain tumour segmentation on MRI images. Our co-training approach utilizes a content and style-matching mechanism to distill the informative features from the full-modality network into a missing modality network. To do so, we encode both full-modality and missing-modality data into a latent space, then we decompose the representation space into a style and content representation. Our style matching module adaptively recalibrates the representation space by learning a matching function to transfer the informative and textural features from a full-modality path into a missing-modality path. Moreover, by modelling the mutual information, our content module surpasses the less informative features and re-calibrates the representation space based on discriminative semantic features. The evaluation process on the BraTS 2018 dataset shows a significant results.

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arXiv2022

Contextual Attention Network: Transformer Meets U-Net

Currently, convolutional neural networks (CNN) (e.g., U-Net) have become the de facto standard and attained immense success in medical image segmentation. However, as a downside, CNN based methods are a double-edged sword as they fail to build long-range dependencies and global context connections due to the limited receptive field that stems from the intrinsic characteristics of the convolution operation. Hence, recent articles have exploited Transformer variants for medical image segmentation tasks which open up great opportunities due to their innate capability of capturing long-range correlations through the attention mechanism. Although being feasibly designed, most of the cohort studies incur prohibitive performance in capturing local information, thereby resulting in less lucidness of boundary areas. In this paper, we propose a contextual attention network to tackle the aforementioned limitations. The proposed method uses the strength of the Transformer module to model the long-range contextual dependency. Simultaneously, it utilizes the CNN encoder to capture local semantic information. In addition, an object-level representation is included to model the regional interaction map. The extracted hierarchical features are then fed to the contextual attention module to adaptively recalibrate the representation space using the local information. Then, they emphasize the informative regions while taking into account the long-range contextual dependency derived by the Transformer module. We validate our method on several large-scale public medical image segmentation datasets and achieve state-of-the-art performance. We have provided the implementation code in https://github.com/rezazad68/TMUnet.

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arXiv2022

Medical Image Segmentation on MRI Images with Missing Modalities: A Review

Dealing with missing modalities in Magnetic Resonance Imaging (MRI) and overcoming their negative repercussions is considered a hurdle in biomedical imaging. The combination of a specified set of modalities, which is selected depending on the scenario and anatomical part being scanned, will provide medical practitioners with full information about the region of interest in the human body, hence the missing MRI sequences should be reimbursed. The compensation of the adverse impact of losing useful information owing to the lack of one or more modalities is a well-known challenge in the field of computer vision, particularly for medical image processing tasks including tumour segmentation, tissue classification, and image generation. Various approaches have been developed over time to mitigate this problem's negative implications and this literature review goes through a significant number of the networks that seek to do so. The approaches reviewed in this work are reviewed in detail, including earlier techniques such as synthesis methods as well as later approaches that deploy deep learning, such as common latent space models, knowledge distillation networks, mutual information maximization, and generative adversarial networks (GANs). This work discusses the most important approaches that have been offered at the time of this writing, examining the novelty, strength, and weakness of each one. Furthermore, the most commonly used MRI datasets are highlighted and described. The main goal of this research is to offer a performance evaluation of missing modality compensating networks, as well as to outline future strategies for dealing with this issue.

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arXiv2021

Multiscale Softmax Cross Entropy for Fovea Localization on Color Fundus Photography

Fovea localization is one of the most popular tasks in ophthalmic medical image analysis, where the coordinates of the center point of the macula lutea, i.e. fovea centralis, should be calculated based on color fundus images. In this work, we treat the localization problem as a classification task, where the coordinates of the x- and y-axis are considered as the target classes. Moreover, the combination of the softmax activation function and the cross entropy loss function is modified to its multiscale variation to encourage the predicted coordinates to be located closely to the ground-truths. Based on color fundus photography images, we empirically show that the proposed multiscale softmax cross entropy yields better performance than the vanilla version and than the mean squared error loss with sigmoid activation, which provides a novel approach for coordinate regression.

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arXiv2021

High-throughput Phenotyping of Nematode Cysts

The beet cyst nematode (BCN) Heterodera schachtii is a plant pest responsible for crop loss on a global scale. Here, we introduce a high-throughput system based on computer vision that allows quantifying BCN infestation and characterizing nematode cysts through phenotyping. After recording microscopic images of soil extracts in a standardized setting, an instance segmentation algorithm serves to detect nematode cysts in these samples. Going beyond fast and precise cyst counting, the image-based approach enables quantification of cyst density and phenotyping of morphological features of cysts under different conditions, providing the basis for high-throughput applications in agriculture and plant breeding research.

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arXiv2021

The Medical Segmentation Decathlon

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD) - a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to non AI experts.

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