SpatialExperiment: molecule-based data

Lukas M. Weber

Leader(s)

Difficulty & duration

  • difficulty: advanced
  • duration: 1-2 weeks

Abstract

One of our core aims is to finalize the SpatialExperiment class structure, so that users can start adopting this for their analysis workflows for data from various spatially resolved transcriptomics platforms.

So far, our current development work and testing has been mainly focused on data from the 10x Genomics Visium platform, which is a “spot-based” platform. (Slide-seqV2 is another spot-based platform.)

We would also like to ensure that our infrastructure can be used with data from “molecule-based” platforms. The major molecule-based platforms include seqFISH (and seqFISH+) and MERFISH.

In this challenge, the aim is to test the current implementation of the SpatialExperiment class to ensure that it can be used to store data from molecule-based platforms.

In particular, seqFISH (and other molecule-based technologies) can measure gene expression at sub-cellular resolution. Storing this information may require some slight modifications to the SpatialExperiment structure. Alternatively, it may be possible to store all the additional information in rowData and colData (and retrieved with spatialCoords).

Targets

This challenge consists of:

  • testing the SpatialExperiment class using a dataset from a molecule-based platform (e.g. seqFISH)
  • creating an example script demonstrating how to store a molecule-based dataset in a SpatialExperiment (see also “Datasets: seqFISH” challenge)
  • if necessary: implement any additional modifications required to the SpatialExperiment class structure

Note there is some overlap with the “Datasets: seqFISH” challenge, where we aim to format a seqFISH dataset into a SpatialExperiment object and provide this to users in the STdata package.

This challenge is relatively open-ended. It may be that the SpatialExperiment class can already handle molecule-based data quite easily (which would make it a short challenge), or alternatively some modifications to the class structure may be required (which would make it a longer challenge).