Thomas Grenier

Author: Thomas

  • Nouveau au département GE ?

    Une petite présentation de l’informatique et des systèmes au département Génie Électrique de l’INSA Lyon. (pdf) Une petite visite des salles à 360° ? ici!

  • Simple Filtering and Segmentation of medical image

    Here is the notebook to start with SimpleITK and basics such as N4 bias field correction on MRI and segmentation using region growing and python programming. We also study the k-means segmentation. Python notebook : (zip)

  • Medical Deep Imaging spring school 2021

    Our third edition of the spring/summer school on deep learning for medical images will be ‘virtual’ and from 19 to 24 of April 2021. Visit the official website here. As the previous edition, there are some lectures, practices, and social events. Most of the content will be available after the school. The first edition web…

  • Install Tensorflow2 or PyTorch/MONAI-dev with conda

    Create a TensorFlow conda environment A short summary of conda utilization: This procedure is the same for PyTorch, just download monai-dev.yml and adapt the previous lines. This file includes MONAI-dev prerequisits. then finalize the MONAI-dev installation by first activate your env and then installing the MOANI-dev using (more information here):

  • A very fast introduction to image processing

    Here are some slides to start with images and fundamental processing (pdf) There are also some funny basic practices using python. You may need to set up a working conda environment. For editing your py files, spyder or PyCharm are nice and efficient python IDEs. Activate a conda environment To create an environment with all…

  • Introduction to UNet for image segmentation (TF1)

    The short introduction to UNet and its architecture (pdf) The proposed code work fine with Tensorflow 1.15 and keras (almostly outdated…). Download this full archive with code, data, and pre-trained model (214 Mo, TP_UNET_FULL.zip). Then, use the notebooks in notebooks_local directory.

  • Medical Deep Imaging spring school 2019

    Do you want to found interesting materials to begin with deep learning for medical applications? Have a look here Materials are in Hands-on session page. Even if you don’t have a GPU card or an efficient installation of frameworks as TensorFlow or PyTorch, you can run the tutorials with your CPU. For beginners (and ones who…

  • Introduction to C and IRQ micro controller programming

    A short introduction to C programming of microcontrollers, including basics for IRQ and ISR design with gnu C. Bare-metal programming. C_uCuP Some sources to understand keywords as static, volatile, extern,… are available in the zip file: sources

  • Cygwin/X ssh X11 forward with OpenGL

    XWin, the X server for cygwin is able to render OpenGL both by software or hardware with direct and indirect context. https://x.cygwin.com/docs/ug/using-glx.html By default, the server uses multiwindow mode, -wgl option (hardware acceleration) and direct context. These choices can lead to encounter troubles when executing remote OpenGL based applications using X11 forwarding on ssh (X and…

  • Spatiotemporal Data Clustering

    We propose a mean-shift formulation allowing spatiotemporal clustering of video streams, and possibly extensible to other multivariate evolving data. Our formulation enables causal or omniscient filtering of spatiotemporal data, which is robust to total object occlusions. It embeds a new clustering algorithm within the filtering procedure that will group samples and reduce their number over…