Input data for Sparrow

Sparrow or Harpy?

Harpy is the successor of Sparrow. Both pipelines were developed by the VIB Saeys Lab. Sparrow was originally build to analyze spatial transcriptomics data and Harpy extends the Sparrow pipeline to also analyze spatial proteomics data.

The pipelines are written in Python and embedded within the scverse, the single cell analysis framework in Python.

To follow the video below you need to use Jupyter notebook 1.explore_sdata.ipynb that can be obtained by running:
git clone https://github.com/vibspatial/targeted_transcriptomics_training.git

The code of this notebook is explained in the videos by Arne Defauw (VIB Spatial Catalyst).

Sparrow input data

You need the following inputs:

• image: DAPI, polyT, membrane staining…
• transcript coordinates: text file with X and Y coordinate of each transcript

Sparrow reads the data and stores it in a SpatialData object, that exist in the memory of your computer when you are working with it. However the SpatialData object is backed by a zarr store that is stored on the disk of your computer. This ensures that you only load the part of the data you’re working on in the memory and not the whole data set.

To follow the code in the video below make sure that you have cloned the full github repository via:
git clone https://github.com/vibspatial/targeted_transcriptomics_training.git