Jussi Tohka

Morteza Ghahremani, Mohammad Khateri, Alejandra Sierra et al.

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.

Juan Miguel Valverde, Artem Shatillo, Jussi Tohka

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.

Mohammad Khateri, Morteza Ghahremani, Alejandra Sierra et al.

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.

Olivier Rukundo, Andrea Behanova, Riccardo De Feo et al.

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.

Gaurang Sharma, Harri Polonen, Juha Pajula et al.

Head Magnetic Resonance Imaging (MRI) is routinely collected and shared for research under strict regulatory frameworks. These frameworks require removing potential identifiers before sharing. But, even after skull stripping, the brain parenchyma contains unique signatures that can match other MRIs from the same participants across databases, posing a privacy risk if additional data features are available. Current regulatory frameworks often mandate evaluating such risks based on the assessment of a certain level of reasonableness. Prior studies have already suggested that a brain MRI could enable participant linkage, but they have relied on training-based or computationally intensive methods. Here, we demonstrate that linking an individual's skull-stripped T1-weighted MRI, which may lead to re-identification if other identifiers are available, is possible using standard preprocessing followed by image similarity computation. Nearly perfect linkage accuracy was achieved in matching data samples across various time intervals, scanner types, spatial resolutions, and acquisition protocols, despite potential cognitive decline, simulating MRI matching across databases. These results aim to contribute meaningfully to the development of thoughtful, forward-looking policies in medical data sharing.

Andrea Behanova, Ali Abdollahzadeh, Ilya Belevich et al.

Background and Objective: Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultrastructure of the brain. In this work, we introduce a freely available Matlab-based gACSON software for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes of brain tissue samples. Methods: The software is equipped with a graphical user interface (GUI). It automatically segments the intra-axonal space of myelinated axons and their corresponding myelin sheaths and allows manual segmentation, proofreading, and interactive correction of the segmented components. gACSON analyzes the morphology of myelinated axons, such as axonal diameter, axonal eccentricity, myelin thickness, or g-ratio. Results: We illustrate the use of the software by segmenting and analyzing myelinated axons in six 3D-EM volumes of rat somatosensory cortex after sham surgery or traumatic brain injury (TBI). Our results suggest that the equivalent diameter of myelinated axons in somatosensory cortex was decreased in TBI animals five months after the injury. Conclusions: Our results indicate that gACSON is a valuable tool for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes. It is freely available at https://github.com/AndreaBehan/g-ACSON under the MIT license.

Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo et al.

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.

Juan Miguel Valverde, Jussi Tohka

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.

Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo et al.

We present a fully convolutional neural network (ConvNet), named RatLesNetv2, for segmenting lesions in rodent magnetic resonance (MR) brain images. RatLesNetv2 architecture resembles an autoencoder and it incorporates residual blocks that facilitate its optimization. RatLesNetv2 is trained end to end on three-dimensional images and it requires no preprocessing. We evaluated RatLesNetv2 on an exceptionally large dataset composed of 916 T2-weighted rat brain MRI scans of 671 rats at nine different lesion stages that were used to study focal cerebral ischemia for drug development. In addition, we compared its performance with three other ConvNets specifically designed for medical image segmentation. RatLesNetv2 obtained similar to higher Dice coefficient values than the other ConvNets and it produced much more realistic and compact segmentations with notably fewer holes and lower Hausdorff distance. The Dice scores of RatLesNetv2 segmentations also exceeded inter-rater agreement of manual segmentations. In conclusion, RatLesNetv2 could be used for automated lesion segmentation, reducing human workload and improving reproducibility. RatLesNetv2 is publicly available at https://github.com/jmlipman/RatLesNetv2.

Ali Farki, Elaheh Moradi, Deepika Koundal et al.

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.

Zewen Zhuo, Ilya Belevich, Ville Leinonen et al.

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.

Gaurang Sharma, Elaheh Moradi, Juha Pajula et al.

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.

Albert Belenguer-Llorens, Carlos Sevilla-Salcedo, Jussi Tohka et al.

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.

Mohammad Khateri, Morteza Ghahremani, Alejandra Sierra et al.

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.

Vandad Imani, Elaheh Moradi, Carlos Sevilla-Salcedo et al.

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.

Vandad Imani, Carlos Sevilla-Salcedo, Elaheh Moradi et al.

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.

Carlos Sevilla-Salcedo, Vandad Imani, Pablo M. Olmos et al.

Machine learning techniques typically applied to dementia forecasting lack in their capabilities to jointly learn several tasks, handle time dependent heterogeneous data and missing values. In this paper, we propose a framework using the recently presented SSHIBA model for jointly learning different tasks on longitudinal data with missing values. The method uses Bayesian variational inference to impute missing values and combine information of several views. This way, we can combine different data-views from different time-points in a common latent space and learn the relations between each time-point while simultaneously modelling and predicting several output variables. We apply this model to predict together diagnosis, ventricle volume, and clinical scores in dementia. The results demonstrate that SSHIBA is capable of learning a good imputation of the missing values and outperforming the baselines while simultaneously predicting three different tasks.

Vandad Imani, Mithilesh Prakash, Marzieh Zare et al.

The Alzheimer's Disease Assessment Scale-Cognitive subscale (ADAS-Cog) is a neuropsychological tool that has been designed to assess the severity of cognitive symptoms of dementia. Personalized prediction of the changes in ADAS-Cog scores could help in timing therapeutic interventions in dementia and at-risk populations. In the present work, we compared single and multitask learning approaches to predict the changes in ADAS-Cog scores based on T1-weighted anatomical magnetic resonance imaging (MRI). In contrast to most machine learning-based prediction methods ADAS-Cog changes, we stratified the subjects based on their baseline diagnoses and evaluated the prediction performances in each group. Our experiments indicated a positive relationship between the predicted and observed ADAS-Cog score changes in each diagnostic group, suggesting that T1-weighted MRI has a predictive value for evaluating cognitive decline in the entire AD continuum. We further studied whether correction of the differences in the magnetic field strength of MRI would improve the ADAS-Cog score prediction. The partial least square-based domain adaptation slightly improved the prediction performance, but the improvement was marginal. In summary, this study demonstrated that ADAS-Cog change could be, to some extent, predicted based on anatomical MRI. Based on this study, the recommended method for learning the predictive models is a single-task regularized linear regression due to its simplicity and good performance. It appears important to combine the training data across all subject groups for the most effective predictive models.

Juan Miguel Valverde, Vandad Imani, Ali Abdollahzadeh et al.

Transfer learning refers to machine learning techniques that focus on acquiring knowledge from related tasks to improve generalization in the tasks of interest. In MRI, transfer learning is important for developing strategies that address the variation in MR images. Additionally, transfer learning is beneficial to re-utilize machine learning models that were trained to solve related tasks to the task of interest. Our goal is to identify research directions, gaps of knowledge, applications, and widely used strategies among the transfer learning approaches applied in MR brain imaging. We performed a systematic literature search for articles that applied transfer learning to MR brain imaging. We screened 433 studies and we categorized and extracted relevant information, including task type, application, and machine learning methods. Furthermore, we closely examined brain MRI-specific transfer learning approaches and other methods that tackled privacy, unseen target domains, and unlabeled data. We found 129 articles that applied transfer learning to brain MRI tasks. The most frequent applications were dementia related classification tasks and brain tumor segmentation. A majority of articles utilized transfer learning on convolutional neural networks (CNNs). Only few approaches were clearly brain MRI specific, considered privacy issues, unseen target domains or unlabeled data. We proposed a new categorization to group specific, widely-used approaches. There is an increasing interest in transfer learning within brain MRI. Public datasets have contributed to the popularity of Alzheimer's diagnostics/prognostics and tumor segmentation. Likewise, the availability of pretrained CNNs has promoted their utilization. Finally, the majority of the surveyed studies did not examine in detail the interpretation of their strategies after applying transfer learning, and did not compare to other approaches.

Jussi Tohka, Mark van Gils

Research on decision support applications in healthcare, such as those related to diagnosis, prediction, treatment planning, etc., have seen enormously increased interest recently. This development is thanks to the increase in data availability as well as advances in artificial intelligence and machine learning research. Highly promising research examples are published daily. However, at the same time, there are some unrealistic expectations with regards to the requirements for reliable development and objective validation that is needed in healthcare settings. These expectations may lead to unmet schedules and disappointments (or non-uptake) at the end-user side. It is the aim of this tutorial to provide practical guidance on how to assess performance reliably and efficiently and avoid common traps. Instead of giving a list of do's and don't s, this tutorial tries to build a better understanding behind these do's and don't s and presents both the most relevant performance evaluation criteria as well as how to compute them. Along the way, we will indicate common mistakes and provide references discussing various topics more in-depth.

Ali Abdollahzadeh, Alejandra Sierra, Jussi Tohka

We develop a cylindrical shape decomposition (CSD) algorithm to decompose an object, a union of several tubular structures, into its semantic components. We decompose the object using its curve skeleton and restricted translational sweeps. For that, CSD partitions the curve skeleton into maximal-length sub-skeletons over an orientation cost, each sub-skeleton corresponds to a semantic component. To find the intersection of the tubular components, CSD translationally sweeps the object in decomposition intervals to identify critical points at which the shape of the object changes substantially. CSD cuts the object at critical points and assigns the same label to parts along the same sub-skeleton, thereby constructing a semantic component. The proposed method further reconstructs the acquired semantic components at the intersection of object parts using generalized cylinders. We apply CSD for segmenting axons in large 3D electron microscopy images and decomposing vascular networks and synthetic objects. We show that our proposal is robust to severe surface noise and outperforms state-of-the-art decomposition techniques in its applications.

Juan Miguel Valverde, Vandad Imani, John D. Lewis et al.

We propose a four-layer fully-connected neural network (FNN) for predicting fluid intelligence scores from T1-weighted MR images for the ABCD-challenge. In addition to the volumes of brain structures, the FNN uses cortical WM/GM contrast and cortical thickness at 78 cortical regions. These last two measurements were derived from the T1-weighted MR images using cortical surfaces produced by the CIVET pipeline. The age and gender of the subjects and the scanner manufacturer are also used as features for the learning algorithm. This yielded 283 features provided to the FNN with two hidden layers of 20 and 15 nodes. The method was applied to the data from the ABCD study. Trained with a training set of 3736 subjects, the proposed method achieved a MSE of 71.596 and a correlation of 0.151 in the validation set of 415 subjects. For the final submission, the model was trained with 3568 subjects and it achieved a MSE of 94.0270 in the test set comprised of 4383 subjects.

Syeda Sakira Hassan, Heikki Huttunen, Jari Niemi et al.

We propose a novel classifier accuracy metric: the Bayesian Area Under the Receiver Operating Characteristic Curve (CBAUC). The method estimates the area under the ROC curve and is related to the recently proposed Bayesian Error Estimator. The metric can assess the quality of a classifier using only the training dataset without the need for computationally expensive cross-validation. We derive a closed-form solution of the proposed accuracy metric for any linear binary classifier under the Gaussianity assumption, and study the accuracy of the proposed estimator using simulated and real-world data. These experiments confirm that the closed-form CBAUC is both faster and more accurate than conventional AUC estimators.

Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo et al.

Manual segmentation of rodent brain lesions from magnetic resonance images (MRIs) is an arduous, time-consuming and subjective task that is highly important in pre-clinical research. Several automatic methods have been developed for different human brain MRI segmentation, but little research has targeted automatic rodent lesion segmentation. The existing tools for performing automatic lesion segmentation in rodents are constrained by strict assumptions about the data. Deep learning has been successfully used for medical image segmentation. However, there has not been any deep learning approach specifically designed for tackling rodent brain lesion segmentation. In this work, we propose a novel Fully Convolutional Network (FCN), RatLesNet, for the aforementioned task. Our dataset consists of 131 T2-weighted rat brain scans from 4 different studies in which ischemic stroke was induced by transient middle cerebral artery occlusion. We compare our method with two other 3D FCNs originally developed for anatomical segmentation (VoxResNet and 3D-U-Net) with 5-fold cross-validation on a single study and a generalization test, where the training was done on a single study and testing on three remaining studies. The labels generated by our method were quantitatively and qualitatively better than the predictions of the compared methods. The average Dice coefficient achieved in the 5-fold cross-validation experiment with the proposed approach was 0.88, between 3.7% and 38% higher than the compared architectures. The presented architecture also outperformed the other FCNs at generalizing on different studies, achieving the average Dice coefficient of 0.79.