Project Description

MONAI is a set of open-source, freely available collaborative frameworks built for accelerating research and clinical collaboration in Medical Imaging. The goal is to accelerate the pace of innovation and clinical translation by building a robust software framework that benefits nearly every level of medical imaging, deep learning research, and deployment.

Open Source Design

MONAI is an open-source project. It is built on top of PyTorch and is released under the Apache 2.0 license.

Standardized

Aiming to capture best practices of AI development for healthcare researchers, with an immediate focus on medical imaging.

User Friendly

Providing user-comprehensible error messages and easy to program API interfaces.

Reproducible

Provides reproducibility of research experiments for comparisons against state-of-the-art implementations.

Easy Integration

Designed to be compatible with existing efforts and ease of 3rd party integration for various components.

High Quality

Delivering high-quality software with enterprise-grade development, tutorials for getting started and robust validation & documentation.

Goal for this Hackweek

The goal is to learn MONAI and understand the different deploy alternatives.

Resources

MONAI Bootcamp 2021

MONAI Get started docs

MONAI Github projects

Anyone with interest on Medical applications based on Artificial Intelligence and MLOps in general is welcome to join. No previous knowledge is required.

Looking for hackers with the skills:

mlops ml mlflow pytorch artificial-intelligence kubernetes helm containers k3s

This project is part of:

Hack Week 22

Activity

  • almost 2 years ago: jordimassaguerpla added keyword "k3s" to this project.
  • almost 2 years ago: jordimassaguerpla added keyword "containers" to this project.
  • almost 2 years ago: jordimassaguerpla added keyword "helm" to this project.
  • almost 2 years ago: jordimassaguerpla added keyword "kubernetes" to this project.
  • almost 2 years ago: ybonatakis liked this project.
  • about 2 years ago: jordimassaguerpla started this project.
  • about 2 years ago: jordimassaguerpla added keyword "artificial-intelligence" to this project.
  • about 2 years ago: jordimassaguerpla added keyword "pytorch" to this project.
  • about 2 years ago: jordimassaguerpla added keyword "mlflow" to this project.
  • about 2 years ago: jordimassaguerpla added keyword "ml" to this project.
  • about 2 years ago: jordimassaguerpla added keyword "mlops" to this project.
  • about 2 years ago: jordimassaguerpla originated this project.

  • Comments

    • jordimassaguerpla
      almost 2 years ago by jordimassaguerpla | Reply

      I was able to deploy "Monai deploy" on a SUSE Rancher k3s cluster successfully!

      It took fixing some helm charts plus writing some new ones.

      As a result, I created this Pull Request upstream:

      https://github.com/Project-MONAI/monai-deploy-workflow-manager/pull/666 .

      There you can see there is a README file explaining how to reproduce the setup using k3s, plus the fixed and hew helm charts.

      This project is in the early stages and it is very specialized, which has been a great opportunity to learn a lot!

      The helm charts that have been contributed will let you deploy orthanc, which you can use to visualize x-rays, mri scans, patient data, .... Then you can "push" this to the monai deploy components that, ultimately, will start a container inside your cluster that will create the prediction. This will usually be a segmentation to help you visualize anomalies, and then this will get back to orthanc for your visualization.

    Similar Projects

    Save pytorch models in OCI registries by jguilhermevanz

    Description

    A prerequisite for running applications in a cloud environment is the presence of a container registry. Another common scenario is users performing machine learning workloads in such environments. However, these types of workloads require dedicated infrastructure to run properly. We can leverage these two facts to help users save resources by storing their machine learning models in OCI registries, similar to how we handle some WebAssembly modules. This approach will save users the resources typically required for a machine learning model repository for the applications they need to run.

    Goals

    Allow PyTorch users to save and load machine learning models in OCI registries.

    Resources


    COOTWbot by ngetahun

    Project Description

    At SCC, we have a rotating task of COOTW (Commanding Office of the Week). This task involves responding to customer requests from jira and slack help channels, monitoring production systems and doing small chores. Usually, we have documentation to help the COOTW answer questions and quickly find fixes. Most of these are distributed across github, trello and SUSE Support documentation. The aim of this project is to explore the magic of LLMs and create a conversational bot.

    Goal for this Hackweek

    • Build data ingestion Data source:
      • SUSE KB docs
      • scc github docs
      • scc trello knowledge board
    • Test out new RAG architecture

    • https://gitlab.suse.de/ngetahun/cootwbot


    Save pytorch models in OCI registries by jguilhermevanz

    Description

    A prerequisite for running applications in a cloud environment is the presence of a container registry. Another common scenario is users performing machine learning workloads in such environments. However, these types of workloads require dedicated infrastructure to run properly. We can leverage these two facts to help users save resources by storing their machine learning models in OCI registries, similar to how we handle some WebAssembly modules. This approach will save users the resources typically required for a machine learning model repository for the applications they need to run.

    Goals

    Allow PyTorch users to save and load machine learning models in OCI registries.

    Resources


    kubectl clone: Seamlessly Clone Kubernetes Resources Across Multiple Rancher Clusters and Projects by dpunia

    Description

    kubectl clone is a kubectl plugin that empowers users to clone Kubernetes resources across multiple clusters and projects managed by Rancher. It simplifies the process of duplicating resources from one cluster to another or within different namespaces and projects, with optional on-the-fly modifications. This tool enhances multi-cluster resource management, making it invaluable for environments where Rancher orchestrates numerous Kubernetes clusters.

    Goals

    1. Seamless Multi-Cluster Cloning
      • Clone Kubernetes resources across clusters/projects with one command.
      • Simplifies management, reduces operational effort.

    Resources

    1. Rancher & Kubernetes Docs

      • Rancher API, Cluster Management, Kubernetes client libraries.
    2. Development Tools

      • Kubectl plugin docs, Go programming resources.

    Building and Installing the Plugin

    1. Set Environment Variables: Export the Rancher URL and API token:
    • export RANCHER_URL="https://rancher.example.com"
    • export RANCHER_TOKEN="token-xxxxx:xxxxxxxxxxxxxxxxxxxx"
    1. Build the Plugin: Compile the Go program:
    • go build -o kubectl-clone ./pkg/
    1. Install the Plugin: Move the executable to a directory in your PATH:
    • mv kubectl-clone /usr/local/bin/

    Ensure the file is executable:

    • chmod +x /usr/local/bin/kubectl-clone
    1. Verify the Plugin Installation: Test the plugin by running:
    • kubectl clone --help

    You should see the usage information for the kubectl-clone plugin.

    Usage Examples

    1. Clone a Deployment from One Cluster to Another:
    • kubectl clone --source-cluster c-abc123 --type deployment --name nginx-deployment --target-cluster c-def456 --new-name nginx-deployment-clone
    1. Clone a Service into Another Namespace and Modify Labels:


    Harvester Packer Plugin by mrohrich

    Description

    Hashicorp Packer is an automation tool that allows automatic customized VM image builds - assuming the user has a virtualization tool at their disposal. To make use of Harvester as such a virtualization tool a plugin for Packer needs to be written. With this plugin users could make use of their Harvester cluster to build customized VM images, something they likely want to do if they have a Harvester cluster.

    Goals

    Write a Packer plugin bridging the gap between Harvester and Packer. Users should be able to create customized VM images using Packer and Harvester with no need to utilize another virtualization platform.

    Resources

    Hashicorp documentation for building custom plugins for Packer https://developer.hashicorp.com/packer/docs/plugins/creation/custom-builders

    Source repository of the Harvester Packer plugin https://github.com/m-ildefons/harvester-packer-plugin


    Multi-pod, autoscalable Elixir application in Kubernetes using K8s resources by socon

    Description

    Elixir / Erlang use their own solutions to create clusters that work together. Kubernetes provide its own orchestration. Due to the nature of the BEAM, it looks a very promising technology for applications that run in Kubernetes and requite to be always on, specifically if they are created as web pages using Phoenix.

    Goals

    • Investigate and provide solutions that work in Phoenix LiveView using Kubernetes resources, so a multi-pod application can be used
    • Provide an end to end example that creates and deploy a container from source code.

    Resources

    https://github.com/dwyl/phoenix-liveview-counter-tutorial https://github.com/propedeutica/elixir-k8s-counter


    Introducing "Bottles": A Proof of Concept for Multi-Version CRD Management in Kubernetes by aruiz

    Description

    As we delve deeper into the complexities of managing multiple CRD versions within a single Kubernetes cluster, I want to introduce "Bottles" - a proof of concept that aims to address these challenges.

    Bottles propose a novel approach to isolating and deploying different CRD versions in a self-contained environment. This would allow for greater flexibility and efficiency in managing diverse workloads.

    Goals

    • Evaluate Feasibility: determine if this approach is technically viable, as well as identifying possible obstacles and limitations.
    • Reuse existing technology: leverage existing products whenever possible, e.g. build on top of Kubewarden as admission controller.
    • Focus on Rancher's use case: the ultimate goal is to be able to use this approach to solve Rancher users' needs.

    Resources

    Core concepts:

    • ConfigMaps: Bottles could be defined and configured using ConfigMaps.
    • Admission Controller: An admission controller will detect "bootled" CRDs being installed and replace the resource name used to store them.
    • Aggregated API Server: By analyzing the author of a request, the aggregated API server will determine the correct bottle and route the request accordingly, making it transparent for the user.


    Metrics Server viewer for Kubernetes by bkampen

    This project is finished please visit the github repo below for the tool.

    Description

    Build a CLI tools which can visualize Kubernetes metrics from the metrics-server, so you're able to watch these without installing Prometheus and Grafana on a cluster.

    Goals

    • Learn more about metrics-server
    • Learn more about the inner workings of Kubernetes.
    • Learn more about Go

    Resources

    https://github.com/bvankampen/metrics-viewer


    Enable the containerized Uyuni server to run on different host OS by j_renner

    Description

    The Uyuni server is provided as a container, but we still require it to run on Leap Micro? This is not how people expect to use containerized applications, so it would be great if we tested other host OSs and enabled them by providing builds of necessary tools for (e.g. mgradm). Interesting candidates should be:

    • openSUSE Leap
    • Cent OS 7
    • Ubuntu
    • ???

    Goals

    Make it really easy for anyone to run the Uyuni containerized server on whatever OS they want (with support for containers of course).


    Port the classic browser game HackTheNet to PHP 8 by dgedon

    Description

    The classic browser game HackTheNet from 2004 still runs on PHP 4/5 and MySQL 5 and needs a port to PHP 8 and e.g. MariaDB.

    Goals

    • Port the game to PHP 8 and MariaDB 11
    • Create a container where the game server can simply be started/stopped

    Resources

    • https://github.com/nodeg/hackthenet


    ADS-B receiver with MicroOS by epaolantonio

    I would like to put one of my spare Raspberry Pis to good use, and what better way to see what flies above my head at any time? add-emoji

    There are various ready-to-use distros already set-up to provide feeder data to platforms like Flightradar24, ADS-B Exchange, FlightAware etc... The goal here would be to do it using MicroOS as a base and containerized decoding of ADS-B data (via tools like dump1090) and web frontend (tar1090).

    Goals

    • Create a working receiver using MicroOS as a base, and containers based on Tumbleweed
    • Make it easy to install
    • Optimize for maximum laziness (i.e. it should take care of itself with minimum intervention)

    Resources

    • 1x Small Board Computer capable of running MicroOS
    • 1x RTL2832U DVB-T dongle
    • 1x MicroSD card
    • https://github.com/antirez/dump1090
    • https://github.com/flightaware/dump1090 (dump1090 fork by FlightAware)
    • https://github.com/wiedehopf/tar1090

    Project status (2024-11-22)

    So I'd say that I'm pretty satisfied with how it turned out. I've packaged readsb (as a replacement for dump1090), tar1090, tar1090-db and mlat-client (not used yet).

    Current status:

    • Able to set-up a working receiver using combustion+ignition (web app based on Fuel Ignition)
    • Able to feed to various feeds using the Beast protocol (Airplanes.live, ADSB.fi, ADSB.lol, ADSBExchange.com, Flyitalyadsb.com, Planespotters.net)
    • Able to feed to Flightradar24 (initial-setup available but NOT tested! I've only tested using a key I already had)
    • Local web interface (tar1090) to easily visualize the results
    • Cockpit pre-configured to ease maintenance

    What's missing:

    • MLAT (Multilateration) support. I've packaged mlat-client already, but I have to wire it up
    • FlightAware support

    Give it a go at https://g7.github.io/adsbreceiver/ !

    Project links


    ClusterOps - Easily install and manage your personal kubernetes cluster by andreabenini

    Description

    ClusterOps is a Kubernetes installer and operator designed to streamline the initial configuration and ongoing maintenance of kubernetes clusters. The focus of this project is primarily on personal or local installations. However, the goal is to expand its use to encompass all installations of Kubernetes for local development purposes.
    It simplifies cluster management by automating tasks and providing just one user-friendly YAML-based configuration config.yml.

    Overview

    • Simplified Configuration: Define your desired cluster state in a simple YAML file, and ClusterOps will handle the rest.
    • Automated Setup: Automates initial cluster configuration, including network settings, storage provisioning, special requirements (for example GPUs) and essential components installation.
    • Ongoing Maintenance: Performs routine maintenance tasks such as upgrades, security updates, and resource monitoring.
    • Extensibility: Easily extend functionality with custom plugins and configurations.
    • Self-Healing: Detects and recovers from common cluster issues, ensuring stability, idempotence and reliability. Same operation can be performed multiple times without changing the result.
    • Discreet: It works only on what it knows, if you are manually configuring parts of your kubernetes and this configuration does not interfere with it you can happily continue to work on several parts and use this tool only for what is needed.

    Features

    • distribution and engine independence. Install your favorite kubernetes engine with your package manager, execute one script and you'll have a complete working environment at your disposal.
    • Basic config approach. One single config.yml file with configuration requirements (add/remove features): human readable, plain and simple. All fancy configs managed automatically (ingress, balancers, services, proxy, ...).
    • Local Builtin ContainerHub. The default installation provides a fully configured ContainerHub available locally along with the kubernetes installation. This configuration allows the user to build, upload and deploy custom container images as they were provided from external sources. Internet public sources are still available but local development can be kept in this localhost server. Builtin ClusterOps operator will be fetched from this ContainerHub registry too.
    • Kubernetes official dashboard installed as a plugin, others planned too (k9s for example).
    • Kubevirt plugin installed and properly configured. Unleash the power of classic virtualization (KVM+QEMU) on top of Kubernetes and manage your entire system from there, libvirtd and virsh libs are required.
    • One operator to rule them all. The installation script configures your machine automatically during installation and adds one kubernetes operator to manage your local cluster. From there the operator takes care of the cluster on your behalf.
    • Clean installation and removal. Just test it, when you are done just use the same program to uninstall everything without leaving configs (or pods) behind.

    Planned features (Wishlist / TODOs)

    • Containerized Data Importer (CDI). Persistent storage management add-on for Kubernetes to provide a declarative way of building and importing Virtual Machine Disks on PVCs for


    SUSE AI Meets the Game Board by moio

    Use tabletopgames.ai’s open source TAG and PyTAG frameworks to apply Statistical Forward Planning and Deep Reinforcement Learning to two board games of our own design. On an all-green, all-open source, all-AWS stack!
    A chameleon playing chess in a train car, as a metaphor of SUSE AI applied to games


    Results: Infrastructure Achievements

    We successfully built and automated a containerized stack to support our AI experiments. This included:

    A screenshot of k9s and nvtop showing PyTAG running in Kubernetes with GPU acceleration

    ./deploy.sh and voilà - Kubernetes running PyTAG (k9s, above) with GPU acceleration (nvtop, below)

    Results: Game Design Insights

    Our project focused on modeling and analyzing two card games of our own design within the TAG framework:

    • Game Modeling: We implemented models for Dario's "Bamboo" and Silvio's "Totoro" and "R3" games, enabling AI agents to play thousands of games ...in minutes!
    • AI-driven optimization: By analyzing statistical data on moves, strategies, and outcomes, we iteratively tweaked the game mechanics and rules to achieve better balance and player engagement.
    • Advanced analytics: Leveraging AI agents with Monte Carlo Tree Search (MCTS) and random action selection, we compared performance metrics to identify optimal strategies and uncover opportunities for game refinement .

    Cards from the three games

    A family picture of our card games in progress. From the top: Bamboo, Totoro, R3

    Results: Learning, Collaboration, and Innovation

    Beyond technical accomplishments, the project showcased innovative approaches to coding, learning, and teamwork:

    • "Trio programming" with AI assistance: Our "trio programming" approach—two developers and GitHub Copilot—was a standout success, especially in handling slightly-repetitive but not-quite-exactly-copypaste tasks. Java as a language tends to be verbose and we found it to be fitting particularly well.
    • AI tools for reporting and documentation: We extensively used AI chatbots to streamline writing and reporting. (Including writing this report! ...but this note was added manually during edit!)
    • GPU compute expertise: Overcoming challenges with CUDA drivers and cloud infrastructure deepened our understanding of GPU-accelerated workloads in the open-source ecosystem.
    • Game design as a learning platform: By blending AI techniques with creative game design, we learned not only about AI strategies but also about making games fun, engaging, and balanced.

    Last but not least we had a lot of fun! ...and this was definitely not a chatbot generated line!

    The Context: AI + Board Games


    ClusterOps - Easily install and manage your personal kubernetes cluster by andreabenini

    Description

    ClusterOps is a Kubernetes installer and operator designed to streamline the initial configuration and ongoing maintenance of kubernetes clusters. The focus of this project is primarily on personal or local installations. However, the goal is to expand its use to encompass all installations of Kubernetes for local development purposes.
    It simplifies cluster management by automating tasks and providing just one user-friendly YAML-based configuration config.yml.

    Overview

    • Simplified Configuration: Define your desired cluster state in a simple YAML file, and ClusterOps will handle the rest.
    • Automated Setup: Automates initial cluster configuration, including network settings, storage provisioning, special requirements (for example GPUs) and essential components installation.
    • Ongoing Maintenance: Performs routine maintenance tasks such as upgrades, security updates, and resource monitoring.
    • Extensibility: Easily extend functionality with custom plugins and configurations.
    • Self-Healing: Detects and recovers from common cluster issues, ensuring stability, idempotence and reliability. Same operation can be performed multiple times without changing the result.
    • Discreet: It works only on what it knows, if you are manually configuring parts of your kubernetes and this configuration does not interfere with it you can happily continue to work on several parts and use this tool only for what is needed.

    Features

    • distribution and engine independence. Install your favorite kubernetes engine with your package manager, execute one script and you'll have a complete working environment at your disposal.
    • Basic config approach. One single config.yml file with configuration requirements (add/remove features): human readable, plain and simple. All fancy configs managed automatically (ingress, balancers, services, proxy, ...).
    • Local Builtin ContainerHub. The default installation provides a fully configured ContainerHub available locally along with the kubernetes installation. This configuration allows the user to build, upload and deploy custom container images as they were provided from external sources. Internet public sources are still available but local development can be kept in this localhost server. Builtin ClusterOps operator will be fetched from this ContainerHub registry too.
    • Kubernetes official dashboard installed as a plugin, others planned too (k9s for example).
    • Kubevirt plugin installed and properly configured. Unleash the power of classic virtualization (KVM+QEMU) on top of Kubernetes and manage your entire system from there, libvirtd and virsh libs are required.
    • One operator to rule them all. The installation script configures your machine automatically during installation and adds one kubernetes operator to manage your local cluster. From there the operator takes care of the cluster on your behalf.
    • Clean installation and removal. Just test it, when you are done just use the same program to uninstall everything without leaving configs (or pods) behind.

    Planned features (Wishlist / TODOs)

    • Containerized Data Importer (CDI). Persistent storage management add-on for Kubernetes to provide a declarative way of building and importing Virtual Machine Disks on PVCs for