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Platform: 10x Visium HD (--platform 10x_visium_hd)

Built-in profile. Ingest runs sge_convert. Point --in-dir at the Space Ranger outs/ directory. Coordinates are scaled by 2 automatically (--scale-xy 2.0 at ingest, --sge-scale 2 at packaging).

Expected inputs (under --in-dir)

Purpose Path under --in-dir
Scale factors binned_outputs/square_002um/spatial/scalefactors_json.json
Count matrix binned_outputs/square_002um/filtered_feature_bc_matrix/
Bin positions binned_outputs/square_002um/spatial/tissue_positions.parquet
Square layers binned_outputs/square_008um, binned_outputs/square_016um (imported if present)
Segmented cells segmented_outputs/ (imported if present)
H&E image Provided per sample via the hne column / config field; µm/pixel read from the 2 µm scalefactors_json.json

Defaults: FICTURE width=12, n_factor=24,48,96, decode_scale=2; packaging with --use-pmpoint --bin-count 500 --sge-scale 2.

1. Single sample (direct CLI)

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cartloader run_together --platform 10x_visium_hd \
    --in-dir /data/visiumhd/sample/outs --out-dir OUT \
    --width 12 --n-factor 48 -j 8 --threads 8

Square (8/16 µm) and segmented-cell layers are imported automatically when present.

H&E is not inside the standard bin layout, so name it. Single sample, inline:

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cartloader run_together --platform 10x_visium_hd \
    --in-dir /data/visiumhd/sample/outs --out-dir OUT \
    --image type=hne,source=/data/visiumhd/sample/he.tif --width 12 --n-factor 48

2. Multi-sample (sample sheet)

One joint model; add a per-sample hne column for the H&E layer:

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cartloader run_together --platform 10x_visium_hd \
    --samples samples.tsv --out-dir OUT --width 12 --n-factor 48 -j 8

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id      in_dir                       hne
s1      /data/visiumhd/s1/outs       /data/visiumhd/s1/he.tif
s2      /data/visiumhd/s2/outs       /data/visiumhd/s2/he.tif

3. Full config (JSON)

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cartloader run_together --platform 10x_visium_hd --config run.json

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// run.json
{
  "platform": "10x_visium_hd", "out_dir": "OUT",
  "resources": { "n_jobs": 8, "threads": 16 },
  "samples": [
    { "id": "s1", "in_dir": "/data/visiumhd/s1/outs", "hne": "/data/visiumhd/s1/he.tif" },
    { "id": "s2", "in_dir": "/data/visiumhd/s2/outs", "hne": "/data/visiumhd/s2/he.tif" }
  ],
  "ficture": [ { "id": "denovo", "mode": "train", "width": "12", "n_factor": "24,48,96" } ]
}

Notes

  • Automatic scaling. The 2 µm bin coordinates are scaled ×2 at ingest and packaging — you do not set this yourself.
  • H&E is an rgb (passthrough) image; its µm/pixel is read from the 2 µm scalefactors_json.json. See Image Modalities.
  • Square (8/16 µm) and segmented-cell imports are wired by the profile and appended to the catalog when the directories exist.

See also