Fernando Pérez-García

awesome-medical-imaging. Awesome list of software that I use to do research in medical imaging.

unet. "pip install unet": PyTorch Implementation of 1D, 2D and 3D U-Net architecture.

highresnet. PyTorch implementation of HighRes3DNet

vesseg. Brain vessel segmentation using 3D convolutional neural networks

SlicerPyTorch. This extension contains only a module with some tools to install PyTorch inside Slicer, using the best possible version.

staple. Python implementation of the STAPLE segmentation algorithm

SlicerParcellation. 3D Slicer modules for brain segmentation using deep learning.

SlicerTorchIO. 3D Slicer module for TorchIO.

resseg-ijcars. Code, data and model for Pérez-García et al. 2021, "A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections"

miccai-educational-challenge-2019. Tutorial about combining PyTorch and NiftyNet for deep learning and medical image computing

optimally-oriented-flux. Python

resector. Algorithm to simulate resection surgery on brain MRI scans. Published in MICCAI 2020, extended in IJCARS.

SlicerEPISURG. 3D Slicer module to visualize the EPISURG dataset and segment postoperative brain resection cavities using deep learning.

resseg. RESSEG: automatic segmentation of postoperative brain cavities on 3D MRI using deep learning.

arduino-claw-crane. Collaboration with artist Estefanía B. Flores for her master's thesis at Goldsmiths, University of London.

gestures-miccai-2021. Code for "Pérez-García et al. 2021, Transfer Learning of Deep Spatiotemporal Networks to Model Arbitrarily Long Videos of Seizures, MICCAI 2021".

jvol. JPEG compression for 3D medical images.

creative-coding. p5.js examples

spotify-bpm-splitter. App to split a Spotify list in children playlists sorted by tempo

ndPytools. Little Python tool to manage Hamamatsu NDPI files

faces-map. Tool to embed faces in a 2D space using computer vision and machine learning

uv2conda. Create a Conda environment file from a Python project using uv.

miccai-educational-challenge-2020. My submission to the MICCAI Educational Challenge 2020.

arterys-models. Python

tf2pt. Jupyter Notebook

vesseg-models. Weights for digital subtraction angiography segmentation

orientations. List of resources to better understand medical images orientation.

azure-tools. azure-tools

telegram-gpt-bot. Use ChatGPT with your voice (in any language) and Telegram.

arduino-acronyms.

phd-thesis-template. TeX

advent-of-code-2022. My solutions for Advent of Code 2022

dcm2niiw. Thin wrapper of dcm2niix with Python and CLI interfaces.

docker-dgx-marc. Dockerfile

blockmatching-nipype. Python

scutoids. Python

slicer-blockmatching. 3D Slicer module as a GUI for blockmatching, a robust registration tool

highresnet-models.

pytorch-tests. Python

url-pdf-img. Python

SlicerAnimation. 3D Slicer module to animate objects using linear transforms

pyblock. Python

cast-coursework. Computer-assisted Surgery and Therapy coursework

slicer-niftyreg. Python