no code implementations • 16 Jan 2024 • Mohammad Khateri, Morteza Ghahremani, Alejandra Sierra, Jussi Tohka
The inability to acquire clean high-resolution (HR) electron microscopy (EM) images over a large brain tissue volume hampers many neuroscience studies.
no code implementations • 12 Jan 2024 • Vandad Imani, Elaheh Moradi, Carlos Sevilla-Salcedo, Vittorio Fortino, Jussi Tohka
Feature selection in noisy label scenarios remains an understudied topic.
no code implementations • 30 Oct 2023 • Olivier Rukundo, Andrea Behanova, Riccardo de Feo, Seppo Ronkko, Joni Oja, Jussi Tohka
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.
no code implementations • 19 Sep 2023 • Mohammad Khateri, Morteza Ghahremani, Alejandra Sierra, Jussi Tohka
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.
1 code implementation • 26 May 2023 • Vandad Imani, Carlos Sevilla-Salcedo, Elaheh Moradi, Vittorio Fortino, Jussi Tohka
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.
1 code implementation • 27 Sep 2022 • Juan Miguel Valverde, Artem Shatillo, Jussi Tohka
We present Sauron, a filter pruning method that eliminates redundant feature maps by discarding the corresponding filters with automatically-adjusted layer-specific thresholds.
1 code implementation • 29 Apr 2022 • Morteza Ghahremani, Mohammad Khateri, Alejandra Sierra, Jussi Tohka
The proposed ADL consists of two auto-encoders: a denoiser and a discriminator.
Ranked #1 on Color Image Denoising on CBSD68 sigma35
no code implementations • 13 Jan 2022 • Carlos Sevilla-Salcedo, Vandad Imani, Pablo M. Olmos, Vanessa Gómez-Verdejo, Jussi Tohka
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.
1 code implementation • 13 Dec 2021 • Andrea Behanova, Ali Abdollahzadeh, Ilya Belevich, Eija Jokitalo, Alejandra Sierra, Jussi Tohka
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.
1 code implementation • 21 Sep 2021 • Vandad Imani, Mithilesh Prakash, Marzieh Zare, Jussi Tohka
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.
1 code implementation • 4 Aug 2021 • Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo, Jussi Tohka
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.
1 code implementation • 3 Aug 2021 • Juan Miguel Valverde, Jussi Tohka
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.
no code implementations • 2 Feb 2021 • Juan Miguel Valverde, Vandad Imani, Ali Abdollahzadeh, Riccardo de Feo, Mithilesh Prakash, Robert Ciszek, Jussi Tohka
We found 129 articles that applied transfer learning to brain MRI tasks.
1 code implementation • 31 Aug 2020 • 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.
4 code implementations • 9 Feb 2020 • Razvan V. Marinescu, Neil P. Oxtoby, Alexandra L. Young, Esther E. Bron, Arthur W. Toga, Michael W. Weiner, Frederik Barkhof, Nick C. Fox, Arman Eshaghi, Tina Toni, Marcin Salaterski, Veronika Lunina, Manon Ansart, Stanley Durrleman, Pascal Lu, Samuel Iddi, Dan Li, Wesley K. Thompson, Michael C. Donohue, Aviv Nahon, Yarden Levy, Dan Halbersberg, Mariya Cohen, Huiling Liao, Tengfei Li, Kaixian Yu, Hongtu Zhu, Jose G. Tamez-Pena, Aya Ismail, Timothy Wood, Hector Corrada Bravo, Minh Nguyen, Nanbo Sun, Jiashi Feng, B. T. Thomas Yeo, Gang Chen, Ke Qi, Shiyang Chen, Deqiang Qiu, Ionut Buciuman, Alex Kelner, Raluca Pop, Denisa Rimocea, Mostafa M. Ghazi, Mads Nielsen, Sebastien Ourselin, Lauge Sorensen, Vikram Venkatraghavan, Keli Liu, Christina Rabe, Paul Manser, Steven M. Hill, James Howlett, Zhiyue Huang, Steven Kiddle, Sach Mukherjee, Anais Rouanet, Bernd Taschler, Brian D. M. Tom, Simon R. White, Noel Faux, Suman Sedai, Javier de Velasco Oriol, Edgar E. V. Clemente, Karol Estrada, Leon Aksman, Andre Altmann, Cynthia M. Stonnington, Yalin Wang, Jianfeng Wu, Vivek Devadas, Clementine Fourrier, Lars Lau Raket, Aristeidis Sotiras, Guray Erus, Jimit Doshi, Christos Davatzikos, Jacob Vogel, Andrew Doyle, Angela Tam, Alex Diaz-Papkovich, Emmanuel Jammeh, Igor Koval, Paul Moore, Terry J. Lyons, John Gallacher, Jussi Tohka, Robert Ciszek, Bruno Jedynak, Kruti Pandya, Murat Bilgel, William Engels, Joseph Cole, Polina Golland, Stefan Klein, Daniel C. Alexander
TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease.
1 code implementation • 24 Jan 2020 • Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo, Olli Gröhn, Alejandra Sierra, Jussi Tohka
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.
3 code implementations • 1 Nov 2019 • 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.
no code implementations • 9 Sep 2019 • Juan Miguel Valverde, Vandad Imani, John D. Lewis, Jussi Tohka
These last two measurements were derived from the T1-weighted MR images using cortical surfaces produced by the CIVET pipeline.
no code implementations • 23 Aug 2019 • Syeda Sakira Hassan, Heikki Huttunen, Jari Niemi, Jussi Tohka
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.
no code implementations • 23 Aug 2019 • Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo, Olli Gröhn, Alejandra Sierra, Jussi Tohka
Several automatic methods have been developed for different human brain MRI segmentation, but little research has targeted automatic rodent lesion segmentation.