arXiv subjects

Jussi Tohka

Publications and source records attributed to Jussi Tohka.

At least 19 recordsLinked to original sources

arXiv2026

Cross-Dataset Linkage of Brain MRI using Image Similarity Measures

Head magnetic resonance imaging (MRI) data are routinely collected and shared for research under strict regulatory frameworks that require the removal of direct identifiers prior to data release. However, even after skull stripping, brain parenchyma may retain participant-specific features that enable linkage of scans acquired from the same individual across datasets, posing a potential privacy risk when combined with auxiliary information. Current regulatory approaches typically assess such risks using qualitative notions of reasonableness. Although prior work has suggested that brain MRI can support subject linkage, existing demonstrations have relied on training-based or computationally intensive methods. Here, we show that reliable linkage of skull-stripped T1-weighted brain MRI is possible using standard preprocessing pipelines followed by direct image similarity computations. Using this simple approach, we achieve near-perfect matching accuracy across datasets acquired at different time points, with varying scanner types, spatial resolutions, and acquisition protocols, and even in the presence of cognitive decline. These experiments simulate realistic scenarios of cross-database matching in large-scale neuroimaging repositories. Our findings highlight a previously underappreciated re-identification risk in shared brain MRI data and provide empirical evidence relevant to the development of informed, forward-looking data-sharing policies in neuroimaging research.

cs.CV↗

arXiv2026

USFetal: Tools for Fetal Brain Ultrasound Compounding

Ultrasound offers a safe, cost-effective, and widely accessible technology for fetal brain imaging, making it especially suitable for routine clinical use. However, it suffers from view-dependent artifacts, operator variability, and a limited field of view, which make interpretation and quantitative evaluation challenging. Ultrasound compounding aims to overcome these limitations by integrating complementary information from multiple 3D acquisitions into a single, coherent volumetric representation. This work provides four main contributions: (1) We present the first systematic categorization of computational strategies for fetal brain ultrasound compounding, including both classical techniques and modern learning-based frameworks. (2) We implement and compare representative methods across four key categories - multi-scale, transformation-based, variational, and deep learning approaches - emphasizing their core principles and practical advantages. (3) Motivated by the lack of full-view, artifact-free ground truth required for supervised learning, we focus on unsupervised and self-supervised strategies and introduce two new deep learning based approaches: a self-supervised compounding framework and an adaptation of unsupervised deep plug-and-play priors for compounding. (4) We conduct a comprehensive evaluation on ten multi-view fetal brain ultrasound datasets, using both expert radiologist scoring and standard quantitative image-quality metrics. We also release the USFetal Compounding Toolbox, publicly available to support benchmarking and future research. Keywords: Ultrasound compounding, fetal brain, deep learning, self-supervised, unsupervised.

eess.IV↗

arXiv2025

MRI Super-Resolution with Deep Learning: A Comprehensive Survey

High-resolution (HR) magnetic resonance imaging (MRI) is crucial for many clinical and research applications. However, achieving it remains costly and constrained by technical trade-offs and experimental limitations. Super-resolution (SR) presents a promising computational approach to overcome these challenges by generating HR images from more affordable low-resolution (LR) scans, potentially improving diagnostic accuracy and efficiency without requiring additional hardware. This survey reviews recent advances in MRI SR techniques, with a focus on deep learning (DL) approaches. It examines DL-based MRI SR methods from the perspectives of computer vision, computational imaging, inverse problems, and MR physics, covering theoretical foundations, architectural designs, learning strategies, benchmark datasets, and performance metrics. We propose a systematic taxonomy to categorize these methods and present an in-depth study of both established and emerging SR techniques applicable to MRI, considering unique challenges in clinical and research contexts. We also highlight open challenges and directions that the community needs to address. Additionally, we provide a collection of essential open-access resources, tools, and tutorials, available on our GitHub: https://github.com/mkhateri/Awesome-MRI-Super-Resolution. IEEE keywords: MRI, Super-Resolution, Deep Learning, Computational Imaging, Inverse Problem, Survey.

eess.IV↗

arXiv2025

Forecasting Future Anatomies: Longitudinal Brain Mri-to-Mri Prediction

Predicting future brain state from a baseline magnetic resonance image (MRI) is a central challenge in neuroimaging and has important implications for studying neurodegenerative diseases such as Alzheimer's disease (AD). Most existing approaches predict future cognitive scores or clinical outcomes, such as conversion from mild cognitive impairment to dementia. Instead, here we investigate longitudinal MRI image-to-image prediction that forecasts a participant's entire brain MRI several years into the future, intrinsically modeling complex, spatially distributed neurodegenerative patterns. We implement and evaluate five deep learning architectures (UNet, U2-Net, UNETR, Time-Embedding UNet, and ODE-UNet) on two longitudinal cohorts (ADNI and AIBL). Predicted follow-up MRIs are directly compared with the actual follow-up scans using metrics that capture global similarity and local differences. The best performing models achieve high-fidelity predictions, and all models generalize well to an independent external dataset, demonstrating robust cross-cohort performance. Our results indicate that deep learning can reliably predict participant-specific brain MRI at the voxel level, offering new opportunities for individualized prognosis.

cs.CV↗

arXiv2025

Federated Learning for Predicting Mild Cognitive Impairment to Dementia Conversion

Dementia is a progressive condition that impairs an individual's cognitive health and daily functioning, with mild cognitive impairment (MCI) often serving as its precursor. The prediction of MCI to dementia conversion has been well studied, but previous studies have almost always focused on traditional Machine Learning (ML) based methods that require sharing sensitive clinical information to train predictive models. This study proposes a privacy-enhancing solution using Federated Learning (FL) to train predictive models for MCI to dementia conversion without sharing sensitive data, leveraging socio demographic and cognitive measures. We simulated and compared two network architectures, Peer to Peer (P2P) and client-server, to enable collaborative learning. Our results demonstrated that FL had comparable predictive performance to centralized ML, and each clinical site showed similar performance without sharing local data. Moreover, the predictive performance of FL models was superior to site specific models trained without collaboration. This work highlights that FL can eliminate the need for data sharing without compromising model efficacy.

cs.LG↗

arXiv2024

Unified Bayesian representation for high-dimensional multi-modal biomedical data for small-sample classification

We present BALDUR, a novel Bayesian algorithm designed to deal with multi-modal datasets and small sample sizes in high-dimensional settings while providing explainable solutions. To do so, the proposed model combines within a common latent space the different data views to extract the relevant information to solve the classification task and prune out the irrelevant/redundant features/data views. Furthermore, to provide generalizable solutions in small sample size scenarios, BALDUR efficiently integrates dual kernels over the views with a small sample-to-feature ratio. Finally, its linear nature ensures the explainability of the model outcomes, allowing its use for biomarker identification. This model was tested over two different neurodegeneration datasets, outperforming the state-of-the-art models and detecting features aligned with markers already described in the scientific literature.

stat.ML↗

arXiv2024

Segment Anything for Dendrites from Electron Microscopy

Segmentation of cellular structures in electron microscopy (EM) images is fundamental to analyzing the morphology of neurons and glial cells in the healthy and diseased brain tissue. Current neuronal segmentation applications are based on convolutional neural networks (CNNs) and do not effectively capture global relationships within images. Here, we present DendriteSAM, a vision foundation model based on Segment Anything, for interactive and automatic segmentation of dendrites in EM images. The model is trained on high-resolution EM data from healthy rat hippocampus and is tested on diseased rat and human data. Our evaluation results demonstrate better mask quality compared to the original and other fine-tuned models, leveraging the features learned during training. This study introduces the first implementation of vision foundation models in dendrite segmentation, paving the path for computer-assisted diagnosis of neuronal anomalies.

cs.CV↗

arXiv2024

Sauron U-Net: Simple automated redundancy elimination in medical image segmentation via filter pruning

We introduce Sauron, a filter pruning method that eliminates redundant feature maps of convolutional neural networks (CNNs). Sauron optimizes, jointly with the loss function, a regularization term that promotes feature maps clustering at each convolutional layer by reducing the distance between feature maps. Sauron then eliminates the filters corresponding to the redundant feature maps by using automatically adjusted layer-specific thresholds. Unlike most filter pruning methods, Sauron requires minimal changes to typical neural network optimization because it prunes and optimizes CNNs jointly, which, in turn, accelerates the optimization over time. Moreover, unlike with other cluster-based approaches, the user does not need to specify the number of clusters in advance, a hyperparameter that is difficult to tune. We evaluated Sauron and five state-of-the-art filter pruning methods on four medical image segmentation tasks. This is an area where little attention has been paid to filter pruning, but where smaller CNN models are desirable for local deployment, mitigating privacy concerns associated with cloud-based solutions. Sauron was the only method that achieved a reduction in model size of over 90% without deteriorating substantially the performance. Sauron also achieved, overall, the fastest models at inference time in machines with and without GPUs. Finally, we show through experiments that the feature maps of models pruned with Sauron are highly interpretable, which is essential for medical image segmentation.

cs.CV↗

arXiv2024

Adversarial Distortion Learning for Medical Image Denoising

We present a novel adversarial distortion learning (ADL) for denoising two- and three-dimensional (2D/3D) biomedical image data. The proposed ADL consists of two auto-encoders: a denoiser and a discriminator. The denoiser removes noise from input data and the discriminator compares the denoised result to its noise-free counterpart. This process is repeated until the discriminator cannot differentiate the denoised data from the reference. Both the denoiser and the discriminator are built upon a proposed auto-encoder called Efficient-Unet. Efficient-Unet has a light architecture that uses the residual blocks and a novel pyramidal approach in the backbone to efficiently extract and re-use feature maps. During training, the textural information and contrast are controlled by two novel loss functions. The architecture of Efficient-Unet allows generalizing the proposed method to any sort of biomedical data. The 2D version of our network was trained on ImageNet and tested on biomedical datasets whose distribution is completely different from ImageNet; so, there is no need for re-training. Experimental results carried out on magnetic resonance imaging (MRI), dermatoscopy, electron microscopy and X-ray datasets show that the proposed method achieved the best on each benchmark. Our implementation and pre-trained models are available at https://github.com/mogvision/ADL.

eess.IV↗

arXiv2024

Multi-Objective Genetic Algorithm for Multi-View Feature Selection

Multi-view datasets offer diverse forms of data that can enhance prediction models by providing complementary information. However, the use of multi-view data leads to an increase in high-dimensional data, which poses significant challenges for the prediction models that can lead to poor generalization. Therefore, relevant feature selection from multi-view datasets is important as it not only addresses the poor generalization but also enhances the interpretability of the models. Despite the success of traditional feature selection methods, they have limitations in leveraging intrinsic information across modalities, lacking generalizability, and being tailored to specific classification tasks. We propose a novel genetic algorithm strategy to overcome these limitations of traditional feature selection methods for multi-view data. Our proposed approach, called the multi-view multi-objective feature selection genetic algorithm (MMFS-GA), simultaneously selects the optimal subset of features within a view and between views under a unified framework. The MMFS-GA framework demonstrates superior performance and interpretability for feature selection on multi-view datasets in both binary and multiclass classification tasks. The results of our evaluations on three benchmark datasets, including synthetic and real data, show improvement over the best baseline methods. This work provides a promising solution for multi-view feature selection and opens up new possibilities for further research in multi-view datasets.

cs.NE↗

arXiv2024

No-Clean-Reference Image Super-Resolution: Application to Electron Microscopy

The inability to acquire clean high-resolution (HR) electron microscopy (EM) images over a large brain tissue volume hampers many neuroscience studies. To address this challenge, we propose a deep-learning-based image super-resolution (SR) approach to computationally reconstruct clean HR 3D-EM with a large field of view (FoV) from noisy low-resolution (LR) acquisition. Our contributions are I) Investigating training with no-clean references for $\ell_2$ and $\ell_1$ loss functions; II) Introducing a novel network architecture, named EMSR, for enhancing the resolution of LR EM images while reducing inherent noise; and, III) Comparing different training strategies including using acquired LR and HR image pairs, i.e., real pairs with no-clean references contaminated with real corruptions, the pairs of synthetic LR and acquired HR, as well as acquired LR and denoised HR pairs. Experiments with nine brain datasets showed that training with real pairs can produce high-quality super-resolved results, demonstrating the feasibility of training with non-clean references for both loss functions. Additionally, comparable results were observed, both visually and numerically, when employing denoised and noisy references for training. Moreover, utilizing the network trained with synthetically generated LR images from HR counterparts proved effective in yielding satisfactory SR results, even in certain cases, outperforming training with real pairs. The proposed SR network was compared quantitatively and qualitatively with several established SR techniques, showcasing either the superiority or competitiveness of the proposed method in mitigating noise while recovering fine details.

cs.CV↗

arXiv2024

Optimizing Feature Selection for Binary Classification with Noisy Labels: A Genetic Algorithm Approach

Feature selection in noisy label scenarios remains an understudied topic. We propose a novel genetic algorithm-based approach, the Noise-Aware Multi-Objective Feature Selection Genetic Algorithm (NMFS-GA), for selecting optimal feature subsets in binary classification with noisy labels. NMFS-GA offers a unified framework for selecting feature subsets that are both accurate and interpretable. We evaluate NMFS-GA on synthetic datasets with label noise, a Breast Cancer dataset enriched with noisy features, and a real-world ADNI dataset for dementia conversion prediction. Our results indicate that NMFS-GA can effectively select feature subsets that improve the accuracy and interpretability of binary classifiers in scenarios with noisy labels.

cs.LG↗

arXiv2024

Volume electron microscopy in injured rat brain validates white matter microstructure metrics from diffusion MRI

Biophysical modeling of diffusion MRI (dMRI) offers the exciting potential of bridging the gap between the macroscopic MRI resolution and microscopic cellular features, effectively turning the MRI scanner into a noninvasive in vivo microscope. In brain white matter, the Standard Model (SM) interprets the dMRI signal in terms of axon dispersion, intra- and extra-axonal water fractions and diffusivities. However, for SM to be fully applicable and correctly interpreted, it needs to be carefully evaluated using histology. Here, we perform a comprehensive histological validation of the SM parameters, by characterizing WM microstructure in sham and injured rat brains using volume (3d) electron microscopy (EM) and ex vivo dMRI. Sensitivity is evaluated by how close each SM metric is to its histological counterpart, and specificity by how independent it is from other, non-corresponding histological features. This comparison reveals that SM is sensitive and specific to microscopic properties, clearing the way for the clinical adoption of in vivo dMRI derived SM parameters as biomarkers for neurological disorders.

physics.bio-ph↗

arXiv2023

Convolutional Neural Networks for Automatic Detection of Intact Adenovirus from TEM Imaging with Debris, Broken and Artefacts Particles

Regular monitoring of the primary particles and purity profiles of a drug product during development and manufacturing processes is essential for manufacturers to avoid product variability and contamination. Transmission electron microscopy (TEM) imaging helps manufacturers predict how changes affect particle characteristics and purity for virus-based gene therapy vector products and intermediates. Since intact particles can characterize efficacious products, it is beneficial to automate the detection of intact adenovirus against a non-intact-viral background mixed with debris, broken, and artefact particles. In the presence of such particles, detecting intact adenoviruses becomes more challenging. To overcome the challenge, due to such a presence, we developed a software tool for semi-automatic annotation and segmentation of adenoviruses and a software tool for automatic segmentation and detection of intact adenoviruses in TEM imaging systems. The developed semi-automatic tool exploited conventional image analysis techniques while the automatic tool was built based on convolutional neural networks and image analysis techniques. Our quantitative and qualitative evaluations showed outstanding true positive detection rates compared to false positive and negative rates where adenoviruses were nicely detected without mistaking them for real debris, broken adenoviruses, and/or staining artefacts.

cs.CV↗

arXiv2023

Self-Supervised Super-Resolution Approach for Isotropic Reconstruction of 3D Electron Microscopy Images from Anisotropic Acquisition

Three-dimensional electron microscopy (3DEM) is an essential technique to investigate volumetric tissue ultra-structure. Due to technical limitations and high imaging costs, samples are often imaged anisotropically, where resolution in the axial direction ($z$) is lower than in the lateral directions $(x,y)$. This anisotropy 3DEM can hamper subsequent analysis and visualization tasks. To overcome this limitation, we propose a novel deep-learning (DL)-based self-supervised super-resolution approach that computationally reconstructs isotropic 3DEM from the anisotropic acquisition. The proposed DL-based framework is built upon the U-shape architecture incorporating vision-transformer (ViT) blocks, enabling high-capability learning of local and global multi-scale image dependencies. To train the tailored network, we employ a self-supervised approach. Specifically, we generate pairs of anisotropic and isotropic training datasets from the given anisotropic 3DEM data. By feeding the given anisotropic 3DEM dataset in the trained network through our proposed framework, the isotropic 3DEM is obtained. Importantly, this isotropic reconstruction approach relies solely on the given anisotropic 3DEM dataset and does not require pairs of co-registered anisotropic and isotropic 3DEM training datasets. To evaluate the effectiveness of the proposed method, we conducted experiments using three 3DEM datasets acquired from brain. The experimental results demonstrated that our proposed framework could successfully reconstruct isotropic 3DEM from the anisotropic acquisition.

eess.IV↗

arXiv2022

Automatic cerebral hemisphere segmentation in rat MRI with lesions via attention-based convolutional neural networks

We present MedicDeepLabv3+, a convolutional neural network that is the first completely automatic method to segment cerebral hemispheres in magnetic resonance (MR) volumes of rats with lesions. MedicDeepLabv3+ improves the state-of-the-art DeepLabv3+ with an advanced decoder, incorporating spatial attention layers and additional skip connections that, as we show in our experiments, lead to more precise segmentations. MedicDeepLabv3+ requires no MR image preprocessing, such as bias-field correction or registration to a template, produces segmentations in less than a second, and its GPU memory requirements can be adjusted based on the available resources. We optimized MedicDeepLabv3+ and six other state-of-the-art convolutional neural networks (DeepLabv3+, UNet, HighRes3DNet, V-Net, VoxResNet, Demon) on a heterogeneous training set comprised by MR volumes from 11 cohorts acquired at different lesion stages. Then, we evaluated the trained models and two approaches specifically designed for rodent MRI skull stripping (RATS and RBET) on a large dataset of 655 MR rat brain volumes. In our experiments, MedicDeepLabv3+ outperformed the other methods, yielding an average Dice coefficient of 0.952 and 0.944 in the brain and contralateral hemisphere regions. Additionally, we show that despite limiting the GPU memory and the training data, our MedicDeepLabv3+ also provided satisfactory segmentations. In conclusion, our method, publicly available at https://github.com/jmlipman/MedicDeepLabv3Plus, yielded excellent results in multiple scenarios, demonstrating its capability to reduce human workload in rat neuroimaging studies.

eess.IV↗

arXiv2022

What Does FEXI Measure?

Filter-exchange imaging (FEXI) has already been utilized in several biomedical studies for evaluating the permeability of cell membranes. The method relies on suppressing the extracellular signal using strong diffusion weighting (the mobility filter causing a reduction in the overall diffusivity) and monitoring the subsequent diffusivity recovery. Using Monte Carlo (MC) simulations, we demonstrate that FEXI is not uniquely sensitive to the transcytolemmal exchange but also to the geometry of involved compartments: Complicated geometry offers locations where spins remain unaffected by the mobility filter; moving to other locations afterward, such spins contribute to the diffusivity recovery without actually permeating any membrane. This exchange mechanism challenges the interpretation of FEXI in complex media such as brain gray matter and opens large room for investigation towards crystallizing the genuine membrane permeation and characterizing the compartment geometry.

physics.med-ph↗

arXiv2022

Region-wise Loss for Biomedical Image Segmentation

We propose Region-wise (RW) loss for biomedical image segmentation. Region-wise loss is versatile, can simultaneously account for class imbalance and pixel importance, and it can be easily implemented as the pixel-wise multiplication between the softmax output and a RW map. We show that, under the proposed RW loss framework, certain loss functions, such as Active Contour and Boundary loss, can be reformulated similarly with appropriate RW maps, thus revealing their underlying similarities and a new perspective to understand these loss functions. We investigate the observed optimization instability caused by certain RW maps, such as Boundary loss distance maps, and we introduce a mathematically-grounded principle to avoid such instability. This principle provides excellent adaptability to any dataset and practically ensures convergence without extra regularization terms or optimization tricks. Following this principle, we propose a simple version of boundary distance maps called rectified Region-wise (RRW) maps that, as we demonstrate in our experiments, achieve state-of-the-art performance with similar or better Dice coefficients and Hausdorff distances than Dice, Focal, weighted Cross entropy, and Boundary losses in three distinct segmentation tasks. We quantify the optimization instability provided by Boundary loss distance maps, and we empirically show that our RRW maps are stable to optimize. The code to run all our experiments is publicly available at: https://github.com/jmlipman/RegionWiseLoss.

eess.IV↗