We have a number of projects lined up, for tools that we urgently want to include into the MCMICRO workflow. Below you can find an overview of these projects. Click on any project to see detailed descriptions, links and the results from the groups.

  • Project 1: Background subtraction

    Description

    This project is geared to add a background subtraction module into the MCMICRO pipeline. It would perform autofluorescence, pixel level subtraction on large .ome.tif images from the Lunaphore...

  • Project 2: MistyR

    Description

    This project aims to implement MistyR as a downstream module into the MCMICRO pipeline.

    Day one of the hackathon

    Setup

    We first evaluated which parts and...

  • Project 3: Starfish

    Description

    This project aims to implement Starfish for image based-transcriptomics processing as module into the MCMICRO pipeline.

    Day one of the hackathon

    Setup

    We first determined, which...

  • Project 4: SpatialData

    Description

    Work in progress, atm the code is not fully implemented.

    This project aims to add SpatialData as an input/output format into the MCMICRO pipeline.

    We worked in two...

  • Project Optional: Artefact Detector

    Description

    This project aims to add an artefact detector the MCMICRO pipeline.