In this notebook we are analysing the results of the project by comparing the classical approaches with the trained model.

Drag-and.-drop app built with Gradio and hosted in a Huggingface space.

A deep-learning pipeline for automated lung segmentation in mice CT scans, aiding lung cancer research by isolating lung regions for more precise analysis.

https://raw.githubusercontent.com/qchapp/lungs-segmentation/refs/heads/master/images/main_fig.png

https://zenodo.org/record/8099852/files/lungs_ct.tif

DeepLabCut Toolbox - DEMO (mouse reaching)

Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans

https://camo.githubusercontent.com/31bd0e2e5b3a6e6abb8eaa6cb2f4284eab6ca727c649a24942a6381ccdc702f7/68747470733a2f2f696d616765732e73717561726573706163652d63646e2e636f6d2f636f6e74656e742f76312f3537663664353163396637343536366635356563663237312f64616564376631362d353237662d343135302d386264642d6362623230653236373435312f636865657461682d657a6769662e636f6d2d766964656f2d746f2d6769662d636f6e7665727465722e6769663f666f726d61743d31383077

https://github.com/DeepLabCut/DeepLabCut/tree/main/examples/Reaching-Mackenzie-2018-08-30/labeled-data/reachingvideo1

https://github.com/DeepLabCut/DeepLabCut/tree/main/examples/openfield-Pranav-2018-10-30/labeled-data/m4s1

GPU ready DeepLabCut image using cuda 12.4

Wide-Depth-Range 6D Object Pose Estimation in Space, CVPR 2021

https://github.com/cvlab-epfl/wide-depth-range-pose/raw/master/resources/SwissCube_Rendering.gif

https://huggingface.co/datasets/EPFL-CVLAB-SPACECRAFT/SwissCube/tree/main

LiftPose3D is a tool for transforming a 2D poses to 3D coordinates on labaratory animals. Test.

https://user-images.githubusercontent.com/20509861/112979625-21cafc80-9159-11eb-8848-93435e7ef68a.gif

https://github.com/NeLy-EPFL/LiftPose3D/tree/master/examples

Dataset provided in the notebook examples

An image analysis tool for the measurement of greyscale orientations from 2D or 3D images

https://epfl-center-for-imaging.gitlab.io/orientationpy/_static/logo.jpg

https://gitlab.com/epfl-center-for-imaging/orientationpy/-/tree/main/data/2D?ref_type=heads

https://gitlab.com/epfl-center-for-imaging/orientationpy/-/tree/main/data/3D?ref_type=heads

The MRS4Brain Toolbox is developed by MRS4Brain research group @ CIBM MRI EPFL AIT and was designed to offer advanced functionalities for Bruker preclinical MRSI data, encompassing preprocessing, fitting, quantification, semi-automatic quality control, co-registration and segmentation of metabolic maps using anatomical images, all conveniently integrated within a single open-source graphical user interface (GUI). The development of this user-friendly toolbox aims to streamline the processing workflow and enhance the accessibility of MRSI for researchers in the preclinical field.

https://www.epfl.ch/labs/mrs4brain/wp-content/uploads/2025/03/MRSIToolbox.jpg

https://github.com/MRS4Brain/MRS4Brain-toolbox/tree/main/Demo/Acquisition%20Data/Demo%20Rat

Find imaging softwares and codes

Pyxu

FAIR level

Popular software

lungs-segmentation

DeepLabCut

wide-depth-range-pose

LiftPose3D

orientationpy

MRS4Brain-toolbox