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Supported Platforms & Inputs

run_together's one-command convenience comes from platform profiles that read each platform's standard output layout automatically. This page is the status hub; each built-in platform has its own page with the exact expected inputs and example commands for all three input modes.

For the profile mechanics (input modes, the canonical config, layer merging), see Specifying Inputs.

Profile status

--platform Profile Ingest Details
10x_xenium ✅ built-in sge_convert Xenium page
10x_visium_hd ✅ built-in sge_convert Visium HD page
cosmx_smi ✅ built-in reformat_cosmx CosMx SMI page
merfish (Vizgen MERSCOPE) ✅ built-in sge_convert (vizgen_merscope) MERSCOPE page
illumina (Illumina StrataMap) ✅ built-in sge_convert (illumina) Illumina StrataMap page
stereoseq (BGI Stereo-seq) ✅ built-in SAW gef2gem + sge_convert (bgi_stereoseq) Stereo-seq page
seqscope (Seq-Scope) ✅ built-in sge_convert (seqscope) Seq-Scope page
pixel_seq, nova_st ⏳ planned sge_convert below
generic (custom CSV/TSV) via custom profile sge_convert below
  • built-in — run_together --platform <name> works with no extra configuration.
  • planned — sge_convert already supports ingest; a run_together profile is not yet shipped.

Built-in platforms

Each page documents the expected input files/columns, the FICTURE/packaging defaults, and example commands for the three input modes (single-sample CLI, sample sheet, config JSON):

  • 10x Xenium — Xenium Ranger directory; morphology images auto-detected; xeniumranger clusters.
  • 10x Visium HD — Space Ranger outs/; automatic ×2 scaling; square + segmented-cell layers; per-sample H&E.
  • CosMx SMI — AtoMx flat-file export via reformat_cosmx; glob-based file matching with overrides.
  • MERSCOPE / MERFISH — individual files or a standard export dir; cell analysis from boundaries, a cell×gene matrix, or an existing cell_id (incl. mixed joint runs).
  • Illumina StrataMap — MEX input with spatial coordinates embedded in the barcode; optional cell boundaries enable cell-level analysis.
  • BGI Stereo-seq — prefix-addressed binary GEFs expanded by SAW (--saw); cell-bin segmentation clustered from its own pixel TSV; registered histology at 0.5 µm/pixel.
  • Seq-Scope — --in-dir is the MEX directory; nanometer barcode coordinates, five-column counts (gene-exon by default); pixel-level only (no segmentation); pre-georeferenced H&E.

Platforms without a built-in profile yet

sge_convert converts every platform in the status table to the unified transcript TSV that FICTURE and packaging consume — the per-platform column names, delimiters, and scaling are already encoded there (see sge_convert). Two ways to run them end-to-end today:

  1. Modules directly — sge_convert → run_ficture2 → run_cartload2. See the platform starter tutorials for worked examples.
  2. A custom run_together profile — copy a built-in profile (assets/run_together_profiles/10x_xenium.json), set ingest.sge_platform to the target platform and adjust the input paths / exclusion regex, then pass it with --platform-json. See Specifying Inputs → Mode 3.

See also