This is an (incomplete) list of software produced in Biomedical Image Analysis group since 2017. Many of these softwares are a result of the collaboration and the main collaborators are linked as well. This list does not contain pipelines to reproduce experiments in various papers.
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RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation |Repo| |Paper| |Main developer|
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Multi-Task U-Net: Automated skull-stripping and segmentation of mouse brain MRI |Repo| |Paper| |Tutorial| |Main developer|
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MU-Net-R: Hippocampus segmentation after brain injury in rat MRI: |Repo| |Main developer| |Collaboration with Epilepsy Research Group at UEF|
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MedicDeepLabV3+: convolutional neural network based on DeepLabv3+ implemented in Python and Pytorch to extract the brain mask and the contralateral hemisphere of rodent MRI brain scans with lesions |Repo| |Preprint| |Main developer|
- gACSON: Matlab-based software is to visualize, segment, and analyze the morphology of neurons in three-dimensional electron microscopy images. |Repo| |Preprint| |Main developer| |Collaboration with Multiscale Imaging Group at UEF|
- DeepACSON: Automated Segmentation of White Matter in 3D Electron Microscopy with Deep Concolutional Networks |Repo| |Paper-DeepACSON| |Paper-CylindericalShapeDecomposition| |Main Developer| |Collaboration with Multiscale Imaging Group at UEF|
- Matlab-based miniTEM-Image-Segmentation equipped with a GUI |Repo| |Main developer|
- A GUI (and Matlab) based fluorescence microspocy image segmentation for TDP-43 translocation analysis |Repo| |Paper||Main developer|
- Region-wise loss for biomedical image segmentation |Repo| |Preprint| |Main developer|
- Sign Consistency Bagging for Variable Importance |Notebook| |Paper|] |Collaboration with Vanessa and Emilio from UC3M|
- Multitask learning for predicting ADAS-Cog scores based on MRI |Repo| |Paper| |Main developer|
- Isc-Toolbox: isc-toolbox: Inter-subject correlation analysis for fMRI in Matlab |Repo| |Paper-group comparison)| |Paper-version 2.0| |Paper-version 1.0| |Paper-evaluation|