Skip to content

Changes

Page history
Added 'contributing' page, updated links authored by Rob Oakes's avatar Rob Oakes
Show whitespace changes
Inline Side-by-side
home.md
View page @ 03d06271
...@@ -12,14 +12,14 @@ Artificial Intelligence in Medical Imaging ...@@ -12,14 +12,14 @@ Artificial Intelligence in Medical Imaging
* [What Is DICOM?](https://www.oak-tree.tech/blog/dicom-primer) DICOM is a file format and network protocol used to store and transport medical images. All modern medical imaging systems such as x-ray, ultrasound, CT, and MRI use it for their data. This article provides an introduction to DICOM for software developers working with medical imaging resources within the Sonador imaging platform. * [What Is DICOM?](https://www.oak-tree.tech/blog/dicom-primer) DICOM is a file format and network protocol used to store and transport medical images. All modern medical imaging systems such as x-ray, ultrasound, CT, and MRI use it for their data. This article provides an introduction to DICOM for software developers working with medical imaging resources within the Sonador imaging platform.
**Components** **Components**
* [Sonador Web Application]() * [Sonador Web Application](https://code.oak-tree.tech/oak-tree/medical-imaging/sonador)
* [Orthanc](https://www.orthanc-server.com/static.php?page=documentation). Orthanc is an open source, light-weight DICOMm server. * [Orthanc](https://www.orthanc-server.com/static.php?page=documentation). Orthanc is an open source, light-weight DICOMm server.
* [OHIF](https://ohif.org/). OHIF is an extensible web imaging platform to create custom DICOM viewers quickly and efficiently. * [OHIF](https://ohif.org/). OHIF is an extensible web imaging platform to create custom DICOM viewers quickly and efficiently.
* [Slicer](https://www.slicer.org/). Sonador IO integrates with 3D Slicer to perform advanced biomedical image analysis. Using Slicer, it is possible to create segmentations for surgical planning, generate training sets for AI, or perform advanced simulation. * [Slicer](https://www.slicer.org/). Sonador IO integrates with 3D Slicer to perform advanced biomedical image analysis. Using Slicer, it is possible to create segmentations for surgical planning, generate training sets for AI, or perform advanced simulation.
* [Airflow](https://airflow.apache.org/). Airflow is a platform to create, schedule, and monitor workflows. Airflow is used within the Sonador project for scheduling data pipelines, training machine learning models, and performing batch tasks on medical imaging data. * [Airflow](https://airflow.apache.org/). Airflow is a platform to create, schedule, and monitor workflows. Airflow is used within the Sonador project for scheduling data pipelines, training machine learning models, and performing batch tasks on medical imaging data.
**Integrations** **Integrations**
* Python * [Python](https://www.python.org/)
- [Sonador IO](https://code.oak-tree.tech/oak-tree/medical-imaging/sonador-client). Sonador IO includes a Python software library for the Orthanc REST API which allows developers to work with imaging resoruces using an object-relational mapping (ORM) interface similar to those provided by the poular web development framework [Django](https://docs.djangoproject.com/en/4.0/topics/db/models/) or [SQLAlchemy](https://www.sqlalchemy.org/). This greatly simplifies the implementation of complex systems and allows for data stored in Orthanc to be integrated with popular Python libraries for machine learning, [Artificial Intelligence](https://pytorch.org/), and [3D processing](https://docs.pyvista.org/). - [Sonador IO](https://code.oak-tree.tech/oak-tree/medical-imaging/sonador-client). Sonador IO includes a Python software library for the Orthanc REST API which allows developers to work with imaging resoruces using an object-relational mapping (ORM) interface similar to those provided by the poular web development framework [Django](https://docs.djangoproject.com/en/4.0/topics/db/models/) or [SQLAlchemy](https://www.sqlalchemy.org/). This greatly simplifies the implementation of complex systems and allows for data stored in Orthanc to be integrated with popular Python libraries for machine learning, [Artificial Intelligence](https://pytorch.org/), and [3D processing](https://docs.pyvista.org/).
- [Sonador AI](https://code.oak-tree.tech/oak-tree/medical-imaging/sonadorai). Sonador AI provides an end-to-end suite of tools and best practice guidance for medical imaging based machine learning. It includes a framework for implementing machine learning moels on top of [PyTorch](https://pytorch.org/), tools for creating annotated datasets, tracking experiments, and model versions, deploying to production, and integrating AI into clinical workflows. - [Sonador AI](https://code.oak-tree.tech/oak-tree/medical-imaging/sonadorai). Sonador AI provides an end-to-end suite of tools and best practice guidance for medical imaging based machine learning. It includes a framework for implementing machine learning moels on top of [PyTorch](https://pytorch.org/), tools for creating annotated datasets, tracking experiments, and model versions, deploying to production, and integrating AI into clinical workflows.
- [Medical Open Network for Artificial Intelligence](https://monai.io/index.html). MONAI is a collection of components and programs designed to build end-to-end AI systems based on medical imaging standards and best practices. Built on top of [PyTorch](https://pytorch.org/), MONAI provides a framework for multi-dimensional medical imaging pipelines; implementations of networks, losses, and evaluation metrics; and support for multi-GPU training. - [Medical Open Network for Artificial Intelligence](https://monai.io/index.html). MONAI is a collection of components and programs designed to build end-to-end AI systems based on medical imaging standards and best practices. Built on top of [PyTorch](https://pytorch.org/), MONAI provides a framework for multi-dimensional medical imaging pipelines; implementations of networks, losses, and evaluation metrics; and support for multi-GPU training.
...@@ -30,19 +30,16 @@ Artificial Intelligence in Medical Imaging ...@@ -30,19 +30,16 @@ Artificial Intelligence in Medical Imaging
## [Development](dev.index) ## [Development](dev.index)
[Sonador Development Quickstart](https://www.oak-tree.tech/blog/sonador-quickstart). Sonador is an open source cloud platform for medical imaging visualization and research. This article shows you how to get started using the Sonador Development Environment. **[Getting Started](https://www.oak-tree.tech/blog/sonador-quickstart)**. Sonador is an open source cloud platform for medical imaging visualization and research. This article shows you how to get started using the Sonador Development Environment.
* Frontend Development * Frontend Development
- [Configuring Sonador to Allow for Remote OHIF Development](https://www.oak-tree.tech/blog/sonador-ohif-config). While Sonador includes a version of OHIF integrated into the platform, it is also possible to configure it allow a remote OHIF instance. - [Configuring Sonador to Allow for Remote OHIF Development](https://www.oak-tree.tech/blog/sonador-ohif-config). While Sonador includes a version of OHIF integrated into the platform, it is also possible to configure it allow a remote OHIF instance.
**[How to Contribute](dev.contributing)**. Thank you for your interest in Sonador! Here are some suggestions on how to help and where to go to collaborate.
## [Deployment](prod.deployment-guide) ## [Deployment](prod.deployment-guide)
<img width="100%" src="uploads/img/sonador.production-deployment.svg"> <img width="100%" src="uploads/img/sonador.production-deployment.svg">
Cluster configuration: storage, networking, and other resources * [Production Deployment Guide](prod.deployment-guide). Preparation, considerations, and process for deploying Sonador for production. _Takes into account both cloud and on-premise deployments._
* [Configuration Options: Sonador and Orthanc.](prod.config) Sonador web applciation and Orthanc application configuration files, options, and deployment strategies.
* [Setup LUKS Encryption for Storage Volumes](setup.luks-encryption) * [Sonador Python Libraries and Packages](deployment.package-repository)
* [Private DICOM Headers Within Orthanc](https://www.oak-tree.tech/blog/soandor-orthanc-private-headers). To allow DICOM to support a broad range of medical imaging software applications, the standard provides for "private tags." This article looks at private tag support within Orthanc and how additional tags can be added.
* [AirFlow Remote Logging Using Object Storage](env-prod.airflow-remote-logging). When running in cloud or container orchestration environments, the default logging configuration for Airflow can result in data loss. This article describes how to configure remote logging to S3 compatible storage.