InnerEye-DeepLearning
InnerEye-DeepLearning copied to clipboard
microsoft
Medical Imaging Deep Learning library to train and deploy 3D segmentation models on Azure Machine Learning
Extract InnerEye Data Module to enable multi-class model: migrate data-related attributes to standalone data module so it can be instantiated without full legacy config [AB#4037](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/4037)
**Currently to run inference/evaluation on a test dataset:** 1. Need to provide run recover ID 2. Need to set "-train=False" **New support will run inference in a new dataset so...
PL has trainer flags to restrict number of batches, this could replace restrict_subjects [AB#3991](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3991)
[AB#3977](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3977)
https://pypi.org/project/vulture/#:~:text=Vulture%20finds%20unused%20code%20in%20Python%20programs.%20This,Vulture%20are%20likely%20to%20miss%20some%20dead%20code. [AB#3953](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3953)
At present, we only have written instructions for how to set up the submodules. It might be easier to have a github project that contains all that sample code, ready...
Classification codepath presently makes hardcoded assumptions about order of channels and segmentations. Move that out of the HDF5 loaders, and make it configurable. [AB#3933](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3933)
* Image sizes * effect of photometric normalization * patch sampling thumbnails Add average Dice to results notebook [AB#3930](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3930)
[AB#3931](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3931)
Add a script that consumes the project settings file, retrieves the AzureML workspace, and with that starts an MLFlow server on localhost. [AB#3929](https://innereye.visualstudio.com/60ce1777-00d6-4015-82bc-488a0c00202f/_workitems/edit/3929)