How do I generate a cloupe file for Visium HD Gene Expression data binned at a size other than 8 µm x 8 µm?

Question: How do I generate a cloupe file for use in Loupe Browser with Visium HD Spatial Gene Expression data binned at a size other than 8 µm x 8 µm?

Answer: By default, Space Ranger count produces a cloupe file for Visium HD Spatial Gene Expression data using 8 µm x 8 µm bins. If you require a cloupe file with a different bin size, then you must use Space Ranger count's --custom-bin-size option when processing the data. When a custom bin size is provided, Space Ranger count creates a cloupe file with 8 µm x 8 µm bins and another cloupe file for custom bin sizes larger than 8 µm x 8 µm. Starting with version 3.1, Space Ranger can generate data for bin sizes smaller than 8 µm x 8 µm (e.g., clustering, differential gene expression, and count matrices), but it will not create a cloupe file for these smaller bin sizes.

For example, the following Space Ranger count command line will generate a cloupe file with 8 µm x 8 µm data binning and a cloupe file with 16 µm x 16 µm data binning:

spaceranger count --id=hd_count \
--transcriptome=/path/to/refdata-gex-GRCh38-2020-A \
--fastqs=/path/to/fastq \
--probe-set=/path/to/Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv \
--slide=H1-YD7CDZK \
--area=A1 \
--cytaimage=/path/to/CAVG10539_2023-11-16_14-56-24_APPS115_H1-YD7CDZK_A1_S11088.tif \
--image=/path/to/APPS115_11088_rescan_01.btf \
--create-bam=false \
--custom-bin-size=16

Products: Visium HD Spatial Gene Expression