What is Space Ranger?

Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images (1).

Space Ranger in Partek® Flow®

Space Ranger 1.3.0 has been wrapped in Partek Flow as Space Ranger task. It does not include all the options and uses cases covered by Space Ranger, but takes .fastq and .jpeg/.tiff files as input and performs alignment, filtering, barcode counting, and UMI counting. The output is gene expression count matrix in a .h5 format (both raw and filtered are available for download via Task Details), which then becomes the starting point for downstream analysis in Partek Flow.

Running Space Ranger in Partek Flow

To run Space Ranger in Partek Flow select Unaligned Reads node on the Analysis tab and then select the Space Ranger task in the toolbox.

If this is the first time you are using Space Ranger or Cell Ranger, you will need to create a Cell Ranger reference (Figure). Click on the Create Cell Ranger 6.0.0 reference button and pick the  Cell Ranger reference name (Figure). Alternatively, Cell Ranger reference can be added beforehand, to the Library file management page (on the Other library files tab).