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@Imaging-Server-Kit

Imaging Server Kit

README.md

EPFL Center for Imaging logo

👋 Welcome!

The Imaging Server Kit is an initiative started by the EPFL Center for Imaging to develop a simple framework for creating and using interoperable image processing algorithms via a client/server system.

serverkit-schema

The kit includes:

  • A collection of algorithms that can be deployed as web servers (with or without Docker) and run from QuPath or Napari, for a wide range of tasks:
Task Examples Napari QuPath
Segmentation StarDist, CellPose, Rembg, SAM-2, InstanSeg ✅ ✅
Object detection Spotiflow, LoG detector ✅ ✅
Vector fields Orientationpy ✅ ✅
Object tracking Trackastra, Trackpy ✅
Image-to-Image SPAM, Noise2Void ✅
Text-to-Image Stable Diffusion ✅
Image-to-Text Image captioning ✅
Classification ResNet50 ✅
  • A Template to easily create new image processing algorithm servers.

The Imaging Server Kit is designed for:

  • Algorithm developers: Test your tools in QuPath or Napari without having to create extensions or plugins.
  • Non-technical Users: Use Python projects without needing to set them up on your computer.

Key Features

  • Server/Client: Run algorithms on a server that you connect to from client apps (Napari, QuPath).
  • Auto-generated UI for algorithm parameters in QuPath and Napari. No need for separate extensions or plugins!
  • Interoperable Algorithms that all accept inputs and express outputs in the same way.
  • Dockerized: Build or pull a Docker image, then start/stop a container to use an algorithm.

Roadmap

March 2025

The Imaging Server Kit is under construction! Here is what we're up to:

  • Make the /info route look nice
  • Screencast a tutorial on how to create a new algorithm server
  • Add a server-side timeout to the /process endpoint
  • Improve the AuthenticatedServer
  • Handle streaming/tiling for processing whole-slide images
  • Add a sample image button in the QuPath extension
  • QuPath extension can send annotations as algo inputs
  • Make a Fiji plugin

Contributors

  • Mallory Wittwer, EPFL Center for Imaging (mallory.wittwer@epfl.ch)
  • Edward Andò, EPFL Center for Imaging
  • Maud Barthélémy, EPFL Center for Imaging
  • Florian Aymanns, EPFL Center for Imaging

Acknowledgements

We acknowledge the Personalized Health and Related Technologies (PHRT) initiative for supporting this project.

Pinned Loading

  1. imaging-server-kit imaging-server-kit Public

    Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.

    Python 2 1

  2. cookiecutter-serverkit cookiecutter-serverkit Public

    Cookiecutter template for creating Imaging Server Kit servers

    Python

  3. qupath-extension-serverkit qupath-extension-serverkit Public

    Run image processing algorithms in QuPath using a client/server interface

    Java 1

  4. napari-serverkit napari-serverkit Public

    Run image processing algorithms in Napari using a client/server interface

    Python 1

  5. serverkit-deploy-docker serverkit-deploy-docker Public

    Reference deployment to run several image processing servers using Docker Compose

Repositories

Showing 10 of 21 repositories
  • cookiecutter-serverkit Public

    Cookiecutter template for creating Imaging Server Kit servers

    Imaging-Server-Kit/cookiecutter-serverkit’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Apr 1, 2025
  • serverkit-deploy-docker Public

    Reference deployment to run several image processing servers using Docker Compose

    Imaging-Server-Kit/serverkit-deploy-docker’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Mar 28, 2025
  • serverkit-trackpy Public

    Implementation of a web server for object tracking using Trackpy.

    Imaging-Server-Kit/serverkit-trackpy’s past year of commit activity
    Python 0 0 0 0 Updated Mar 28, 2025
  • serverkit-trackastra Public

    Implementation of a web server for cell tracking using Trackastra.

    Imaging-Server-Kit/serverkit-trackastra’s past year of commit activity
    Python 0 0 0 0 Updated Mar 28, 2025
  • serverkit-stardist Public

    Implementation of a web server for cell nuclei detection using StarDist.

    Imaging-Server-Kit/serverkit-stardist’s past year of commit activity
    Python 0 1 0 0 Updated Mar 28, 2025
  • serverkit-stable-diffusion Public

    Implementation of a web server for image generation using Stable Diffusion.

    Imaging-Server-Kit/serverkit-stable-diffusion’s past year of commit activity
    Python 1 0 0 0 Updated Mar 28, 2025
  • serverkit-spotiflow Public

    Implementation of a web server for spot detection using Spotiflow.

    Imaging-Server-Kit/serverkit-spotiflow’s past year of commit activity
    Python 0 0 0 0 Updated Mar 28, 2025
  • serverkit-spam Public

    Implementation of a web server for image registration using SPAM.

    Imaging-Server-Kit/serverkit-spam’s past year of commit activity
    Python 0 0 0 0 Updated Mar 28, 2025
  • serverkit-skimage-LoG Public

    Implementation of a web server for blob detection using Scikit-image's LoG detector

    Imaging-Server-Kit/serverkit-skimage-LoG’s past year of commit activity
    Python 0 0 0 0 Updated Mar 28, 2025
  • serverkit-sam2 Public

    Implementation of a web server for image segmentation using SAM 2.

    Imaging-Server-Kit/serverkit-sam2’s past year of commit activity
    Python 1 0 0 0 Updated Mar 28, 2025
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