Skip to content

A tool for all-kinds segmentation in microscopy imaging which encourages data centric approaches

License

Notifications You must be signed in to change notification settings

HelmholtzAI-Consultants-Munich/data-centric-platform

Repository files navigation

Data Centric Platform

A data centric platform for all-kinds segmentation in microscopy imaging

stability-wip tests codecov Documentation Status

How to use this?

This repo includes a client and server side for using our data centric platform. The client and server communicate via the bentoml library. The client interacts with the server every time we run model inference or training. For full functionality of the software the server should be running, either locally or remotely. To install and start the server side follow the instructions described in DCP Server Installation & Launch.

To run the client GUI follow the instructions described in DCP Client Installation & Launch.

DCP handles all kinds of segmentation tasks! Try it out if you need to do:

  • Instance segmentation
  • Semantic segmentation
  • Multi-class instance segmentation

Toy data

This repo includes the data/ directory with some toy data which you can use as the Uncurated dataset folder. You can create (empty) folders for the other two directories required in the welcome window and start playing around.

Enabling data centric development

Our platform encourages the use of data centric practices. With the user friendly client interface you can:

  • Detect and remove outliers from your training data: only confirmed samples are used to train our models
  • Detect and correct labeling errors: editing labels with the integrated napari visualisation tool
  • Establish consensus: allows for multiple annotators before curated label is passed to train model
  • Focus on data curation: no interaction with model parameters during training and inference

Get more with less!

About

A tool for all-kinds segmentation in microscopy imaging which encourages data centric approaches

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published