monailabel-weekly 0.4.dev2211

Active Learning Toolkit for Healthcare Imaging

MONAI Label

MONAI Label is a server-client system that facilitates interactive medical image annotation by using AI. It is an open-source and easy-to-install ecosystem that can run locally on a machine with single or multiple GPUs. Both server and client work on the same/different machine. It shares the same principles with MONAI.

MONAI Label Demo

Features

The codebase is currently under active development.

• Framework for developing and deploying MONAI Label Apps to train and infer AI models
• Compositional & portable APIs for ease of integration in existing workflows
• Customizable labelling app design for varying user expertise
• Annotation support via 3DSlicer & OHIF
• PACS connectivity via DICOMWeb

Installation

MONAI Label supports following OS with GPU/CUDA enabled.

• Ubuntu
• Windows

To install the current release, you can simply run:

  pip install monailabel
  
  # download sample apps/dataset
  monailabel apps --download --name deepedit --output apps
  monailabel datasets --download --name Task09_Spleen --output datasets
  
  # run server
  monailabel start_server --app apps/deepedit --studies datasets/Task09_Spleen/imagesTr

If monailabel install path is not automatically determined, then you can provide explicit install path as:

monailabel apps --prefix ~/.local

For prerequisites, other installation methods (using the default GitHub branch, using Docker, etc.), please refer to the installation guide.

Once you start the MONAI Label Server, by default server will be up and serving at http://127.0.0.1:8000/. Open the serving URL in browser. It will provide you the list of Rest APIs available. For this, please make sure you use the HTTP protocol. HTTPS is not implemented.

3D Slicer

Download Preview Release from https://download.slicer.org/ and install MONAI Label plugin from Slicer Extension Manager.

Refer 3D Slicer plugin for other options to install and run MONAI Label plugin in 3D Slicer.

To avoid accidentally using an older Slicer version, you may want to uninstall any previously installed 3D Slicer package.

OHIF

MONAI Label comes with pre-built plugin for OHIF Viewer. To use OHIF Viewer, you need to provide DICOMWeb instead of FileSystem as studies when you start the server.

Please install Orthanc before using OHIF Viewer. For Ubuntu 20.x, Orthanc can be installed as apt-get install orthanc orthanc-dicomweb. However, you have to upgrade to latest version by following steps mentioned here

You can use PlastiMatch to convert NIFTI to DICOM

  # start server using DICOMWeb
  monailabel start_server --app apps\deepedit --studies http://127.0.0.1:8042/dicom-web

OHIF Viewer will be accessible at http://127.0.0.1:8000/ohif/

NOTE: OHIF does not yet support Multi-Label interaction for DeepEdit.

Pathology using Digital Slide Archive (DSA)

Refer Pathology for running a sample pathology use-case in MONAILabel.

NOTE: The Pathology App and DSA Plugin are under active development.

Contributing

For guidance on making a contribution to MONAI Label, see the contributing guidelines.

Community

Join the conversation on Twitter @ProjectMONAI or join our Slack channel.

Ask and answer questions over on MONAI Label's GitHub Discussions tab.

Links

• Website: https://monai.io/
• API documentation: https://docs.monai.io/projects/label
• Code: https://github.com/Project-MONAI/MONAILabel
• Project tracker: https://github.com/Project-MONAI/MONAILabel/projects
• Issue tracker: https://github.com/Project-MONAI/MONAILabel/issues
• Wiki: https://github.com/Project-MONAI/MONAILabel/wiki
• Test status: https://github.com/Project-MONAI/MONAILabel/actions
• PyPI package: https://pypi.org/project/monailabel/
• Weekly previews: https://pypi.org/project/monailabel-weekly/
• Docker Hub: https://hub.docker.com/r/projectmonai/monailabel