Reference Overview¶

This section documents the CartLoader CLI by task.

SGE Preparation¶

- SGE Format Conversion
  
  sge_convert: Standardize raw platform outputs into the unified format; optional visualization; optional density-based filtering
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- SGE Preparation Add-ons
  
  sge_stitch: Stitch >=2 SGEs into one.
  
  sge_orientate: Reorient SGE by rotation and flips.
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- Single-sample Analysis
  
  run_ficture2: Train spatial factors and decode pixels; writes a manifest for packaging
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- Multi-sample Analysis
  
  run_ficture2_multi: Train spatial factors across >=2 samples and perform per‑sample pixel‑level decoding, writing individual manifests.
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- Feature Customization
  
  feature_filtering: Customize the feature set by list, substring, regex, or type for downstream analysis, e.g., FICTURE
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- Asset Packaging
  
  run_cartload2: Package SGE and (optionally) FICTURE outputs into PMTiles and write a catalog of layers.
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- Multi-sample Packaging
  
  run_cartload2_multi: For each sample, package SGE and (optionally) FICTURE outputs into PMTiles and write a catalog of layers.
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- Import Images
  
  import_image: Convert an image into a georeferenced PMTiles layer (optionally reorient) and register it in the catalog.
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- Import Cell Analysis
  
  import_xenium_cell, import_visiumhd_cell: Import platform‑specific cell analysis outputs and add them to the catalog.
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- AWS Upload
  
  upload_aws: Upload outputs to an S3 bucket for sharing or web visualization.
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- Zenodo Upload
  
  upload_zenodo: Upload outputs to a Zenodo deposition, creating a new draft or updating an existing record.
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- Xenium Pipeline
  
  run_xenium: Xenium Pipeline Orchestrator to run multiple modules together
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- Xenium Pipeline Add-ons
  
  load_xenium_ranger: Scans Xenium Ranger output and writes a JSON manifest of detected assets.
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- Visium HD Pipeline
  
  run_visiumhd: Visium HD Pipeline Orchestrator to run multiple modules together
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- Visium HD Pipeline Add-ons
  
  load_space_ranger: Scans Space Ranger output and writes a JSON manifest of detected assets.
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