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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 Stitching

      sge_stitch: Stitch >=2 SGEs into one.

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    • SGE Reorientation

      sge_orientate: Reorient SGE by rotation and flips.

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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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FICTURE Analysis

    • 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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Asset Packaging

    • 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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Data Repository Upload

    • AWS Upload

      upload_aws: Upload outputs to an S3 bucket for sharing or web visualization.

    Read

    • Zenodo Upload

      upload_zenodo: Upload outputs to a Zenodo deposition, creating a new draft or updating an existing record.

    Read

Platform-Specific Modules

    • 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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