monaibundle

Integration with MONAI Bundle

The App helps to pull any MONAI Bundle from MONAI ZOO. However the following constraints has to be met for any monai bundle to directly import and use in MONAI Label.

• Has to meet MONAI Bundle Specification.
• For Inference, the bundle has defined inference.json or inference.yaml and defines these keys
• For Training, the bundle has defined train.json or train.yaml and defines these keys
• For Multi-GPU Training, the bundle has defined multi_gpu_train.json or multi_gpu_train.yaml

By default models are picked from https://github.com/Project-MONAI/model-zoo/blob/dev/models/model_info.json

Structure of the App

• lib/infers is to define and activate inference task over monai-bundle.
• lib/trainers is to define and activate training task over monai-bundle for single/multi gpu.
• lib/activelearning is the module to define the image selection techniques.
• main.py is the script to extend MONAILabelApp class

Modify Constants defined in Infer and Train to customize and adopt if the basic standard/schema is not met for your bundle.

Overview

How To Use?

# skip this if you have already downloaded the app or using github repository (dev mode)
monailabel apps --download --name monaibundle --output workspace

# List all available models from zoo
monailabel start_server --app workspace/monaibundle --studies workspace/images

# Pick spleen_ct_segmentation_v0.1.0 model
monailabel start_server --app workspace/monaibundle --studies workspace/images --conf models spleen_ct_segmentation_v0.1.0

# Pick spleen_ct_segmentation_v0.1.0 model and preload
monailabel start_server --app workspace/monaibundle --studies workspace/images --conf models spleen_ct_segmentation_v0.1.0 --conf preload true

# Pick DeepEdit And Segmentation model (multiple models)
monailabel start_server --app workspace/monaibundle --studies workspace/images --conf models "spleen_ct_segmentation_v0.1.0,spleen_deepedit_annotation_v0.1.0"

# Pick All
monailabel start_server --app workspace/monaibundle --studies workspace/images --conf models all

# Pick All (Skip Training Tasks or Infer only mode)
monailabel start_server --app workspace/monaibundle --studies workspace/images --conf models all --conf skip_trainers true

Additional Configs

Pass them as --conf name value while starting MONAILabelServer

Name	Values	Description
zoo_info	string	Default value: https://github.com/Project-MONAI/model-zoo/blob/dev/models/model_info.json
zoo_source	string	Default value: github
zoo_repo	string	Default value: Project-MONAI/model-zoo/hosting_storage_v1
preload	true, false	Preload model into GPU
skip_trainers	true, false	Skip adding training tasks (Run in Infer mode only)