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CosMx SMI Starter Tutorial

This tutorial walks through a starter end-to-end workflow for CosMx SMI data using an adult mouse hippocampus subset extracted from a coronal brain section.

It first runs the whole analysis with a single run_together command, then walks through the same analysis step by step: input preparation, SGE format conversion, FICTURE analysis, asset packaging, and data upload.

Run with run_together

Download the example data, hosted on Zenodo (10.5281/zenodo.17953582), into a work directory:

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work_dir=/path/to/work/directory        # replace with your work directory
mkdir -p ${work_dir} && cd ${work_dir}
wget https://zenodo.org/records/17953582/files/cosmxsmi_starter.raw.tar.gz
tar --strip-components=1 -zxvf cosmxsmi_starter.raw.tar.gz   # extracts input.tsv.gz

The CosMx SMI profile expects a full AtoMx flat-file export (transcript, cell-metadata, and polygon files). The starter data is a single transcript table, so it goes through the generic profile with the cosmx_smi input preset of sge_convert (comma-separated; columns x_global_px, y_global_px, target). Write a small config file that selects the preset:

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cat > cosmxsmi_starter.json <<'EOF'
{ "ingest": { "sge_platform": "cosmx_smi" } }
EOF

Then run the pipeline, either with a local installation or with the Docker image:

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cartloader run_together \
  --platform generic \
  --raw-transcript ./input.tsv.gz \
  --config cosmxsmi_starter.json \
  --units-per-um 8.333333 \
  --out-dir ./out/cosmxsmi_hippo \
  --id cosmxsmi_hippo \
  --width 12 \
  --n-factor 6,12 \
  --threads 4 -j 4

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docker run --rm -v ${work_dir}:/data hyunminkang/cartloader:latest \
  run_together \
  --platform generic \
  --raw-transcript /data/input.tsv.gz \
  --config /data/cosmxsmi_starter.json \
  --units-per-um 8.333333 \
  --out-dir /data/out/cosmxsmi_hippo \
  --id cosmxsmi_hippo \
  --width 12 \
  --n-factor 6,12 \
  --threads 4 -j 4

--units-per-um 8.333333 (1000 / 120) converts the 120 nm pixels to µm. The result to deploy is out/cosmxsmi_hippo/cartl/cosmxsmi_hippo/ (a catalog.yaml and the PMTiles it lists). Add --dry-run to print the commands without running them.

How run_together differs from the step-by-step path

  • FICTURE runs through run_ficture2_multi (a joint model over a single sample) with single-molecule pixel decoding, instead of run_ficture2.
  • Feature filters are the run_together defaults: control features (Unassigned, Neg, BLANK/Blank, Intergenic, Deprecated, System, NCS-, NCP-) are dropped at ingest; predicted (Gm<digit>), mitochondrial (mt-/MT-), and ribosomal (Rps/Rpl) genes stay in the data but are left out of the factor models. Change them with --ingest-exclude-feature-regex and --exclude-feature-regex.
  • Point layers are packaged with pmpoint (--use-pmpoint, 500 gene bins) instead of tippecanoe.
  • Outputs go under --out-dir: tsv/<id>/ (converted SGE), fic/ (FICTURE), and cartl/<id>/ (PMTiles and catalog.yaml; deploy this), instead of sge/, ficture2/, and cartload2/.
  • Publishing is built in: --s3-upload uploads cartl/<id>/ to S3 (see Publishing). For Zenodo, run upload_zenodo on cartl/<id>/ as in the step-by-step path.

Step by Step (Individual Commands)

The same analysis, one command at a time. Use it to understand each stage or to customize it.

Set Up the Environment

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# ====
# Replace the placeholders with values for your system.
# ====
work_dir=/path/to/work/directory        # directory holding the input data; outputs are written here too
cd $work_dir

n_jobs=10                               # number of parallel jobs (also used as threads per job below)

# Activate the Python environment in which CartLoader is installed
conda activate ENV_NAME                 # replace ENV_NAME (or: source /path/to/venv/bin/activate)

No tool paths needed

Once submodules/build.sh has run (see Installation), every CartLoader command finds spatula, punkst, tippecanoe, pmtiles, and pmpoint in the submodules/ directory of the repository, and the default color map at assets/default_color_map.tsv. Pass --spatula, --ficture2 (the punkst repository directory, which contains bin/punkst), --tippecanoe, --pmtiles, or --cmap-file only to use a different build or file. upload_aws runs the aws CLI from your PATH (--aws to override).

Input Data

Use the data downloaded above.

NanoString CosMx SMI produces single‑molecule spatial transcriptomics data as a comma‑separated values (CSV) table (input.tsv.gz in the starter data).

CSV File Format

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"fov","cell_ID","x_global_px","y_global_px","x_local_px","y_local_px","z","target","CellComp"
64,0,-473043,7954.533,4015.3,4246.2,1,"Gfap","None"
64,0,-473022.9,7902.723,4035.48,4194.39,1,"Fth1","None"
64,0,-473132,7836.476,3926.34,4128.143,1,"Ptn","None"
  • fov: The field of view (FOV) number.
  • cell_ID: Unique identifier for a single cell within a given FOV; 0 if background or unassigned molecules.
  • x_global_px, y_global_px: Global pixel coordinates relative to the tissue.
  • x_local_px, y_local_px: The x or y position (in pixels) relative to the given FOV.
  • z: Z-plane index representing the depth (optical section) where the transcript was detected.
  • target: Target name.
  • CellComp: Subcellular location of the target.

Define ID and Parameters

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# Unique identifier for your dataset
DATA_ID="cosmxsmi_hippo"                # change this to reflect your dataset name
PLATFORM="cosmx_smi"                    # platform information
SCALE=$(echo 1000/120|bc -l)            # coordinate units per micrometer

# LDA parameters
train_width=12                           # define LDA training hexagon width (comma-separated if multiple widths are applied)
n_factor=6,12                            # define number of factors in LDA training (comma-separated if multiple n-factor values are provided)

How to define Scaling Factors for CosMx SMI?

According to the README.html provided with the example CosMx dataset, each pixel has an edge length of 120 nm. To calculate the number of pixels per micrometer, use the formula: scale = 1000 / 120.

SGE Format Conversion

Convert the raw input to the unified SGE format. See more details in its Reference page.

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cartloader sge_convert \
  --makefn sge_convert.mk \
  --platform ${PLATFORM} \
  --in-csv ./input.tsv.gz \
  --units-per-um ${SCALE} \
  --out-dir ./sge \
  --exclude-feature-regex '^(BLANK|Neg|Intergenic|Deprecated|Unassigned)' \
  --sge-visual \
  --n-jobs ${n_jobs}
Parameter Required Type Description
--platform required string Input platform, which sets the default input columns and delimiter (options: 10x_visium_hd, seqscope, illumina, 10x_xenium, bgi_stereoseq, cosmx_smi, vizgen_merscope, pixel_seq, nova_st, generic)
--in-csv required string Path to the input transcript CSV/TSV file
--out-dir required string Output directory for the converted SGE files
--units-per-um float Coordinate units per µm in the input (default: 1, i.e. already in µm; 1000 for the Seq-Scope raw TSV; detected from the barcodes for illumina)
--csv-colname-feature-name string Gene-name column in the input (default: set by --platform)
--csv-colname-count string Count column in the input (default: set by --platform; without one, each row counts 1)
--makefn string File name for the generated Makefile (default: sge_convert.mk)
--exclude-feature-regex regex Pattern of feature names to drop (e.g. control probes)
--sge-visual flag Draw the converted SGE as an image (xy.png) for a visual check
--n-jobs int Number of parallel jobs (default: 1)

FICTURE Analysis

Compute spatial factors using punkst (FICTURE2). See more details on the Reference page.

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cartloader run_ficture2 \
  --makefn run_ficture2.mk \
  --main \
  --in-transcript ./sge/transcripts.unsorted.tsv.gz \
  --in-feature ./sge/feature.clean.tsv.gz \
  --in-minmax ./sge/coordinate_minmax.tsv \
  --exclude-feature-regex '^(mt-.*$|Gm\d+$)' \
  --out-dir ./ficture2 \
  --width ${train_width} \
  --n-factor ${n_factor} \
  --n-jobs ${n_jobs} \
  --threads ${n_jobs}
Parameter Required Type Description
--main required 1 flag Run all five main steps
--in-transcript required string Path to the transcript-indexed SGE file from sge_convert
--out-dir required string Output directory
--width required int or comma-separated list Hexagon width(s) in µm for LDA training
--n-factor required int or comma-separated list Number(s) of LDA factors; one model per width × factor combination
--makefn string File name for the generated Makefile (default: run_ficture2.mk)
--in-feature string Path to the per-gene count file from sge_convert (default: the feature list made during tiling)
--in-minmax string Path to the coordinate min/max file from sge_convert (default: the range computed during tiling)
--exclude-feature-regex regex Feature names to leave out of the factor analysis. punkst matches the whole name, so end each alternative with .* or $ as needed (the example drops mitochondrial mt-* and predicted Gm<digits> genes)
--cmap-file string Color map TSV (default: assets/default_color_map.tsv in the CartLoader repository)
--n-jobs int Number of parallel jobs (default: 1)
--threads int Number of threads per job (default: 4)

1: CartLoader requires at least one action: --tile (tiling), --segment (hexagon segmentation), --init-lda (LDA training), --decode (pixel-level decoding), --umap (UMAP of the factors), or --main for all five.

CartLoader Asset Packaging

Package the SGE and the FICTURE results into PMTiles and a catalog.yaml for CartoScope. See more details in its Reference page.

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cartloader run_cartload2 \
  --makefn run_cartload2.mk \
  --fic-dir ./ficture2 \
  --out-dir ./cartload2 \
  --id ${DATA_ID} \
  --n-jobs ${n_jobs} \
  --threads ${n_jobs}

Packaging without factor analysis

To host only the SGE (no factors), use cartloader run_together ... --no-ficture, which tiles the transcripts and packages them without training any model.

Parameter Required Type Description
--fic-dir required string FICTURE output directory from run_ficture2; must contain ficture.params.json (the SGE paths are read from it)
--out-dir required string Output directory for the PMTiles, assets, and catalog.yaml
--id required string Dataset ID used in the catalog and output metadata (no whitespace)
--makefn string File name for the generated Makefile (default: run_cartload2.mk)
--n-jobs int Number of parallel jobs (default: 1)
--threads int Number of threads per job (default: 4)
--spatula, --tippecanoe, --pmtiles string Tool paths (default: the copies built under submodules/)

Upload to Data Repository

Choose a data repository to host/share your output

CartLoader supports two upload options (AWS and Zenodo) for storing PMTiles of SGE and spatial factors in a data repository.

Choose the one that best suits your needs.

Upload the generated CartLoader outputs to your designated AWS S3 directory. The aws CLI must be configured with credentials that can write there (see AWS Upload Failures).

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# AWS S3 target location
S3_DIR=s3://your-bucket/path/to/dir     # recommended: end with DATA_ID, e.g. s3://your-bucket/test-data/${DATA_ID}

cartloader upload_aws \
  --in-dir ./cartload2 \
  --s3-dir "${S3_DIR}" \
  --n-jobs ${n_jobs}
Parameter Required Type Description
--in-dir required string Directory with the CartLoader packaging output (containing catalog.yaml)
--s3-dir required string Target S3 directory
--profile string AWS CLI profile to use
--aws string Path to the AWS CLI (default: aws)
--n-jobs int Number of parallel jobs (default: 2)

Upload the generated CartLoader outputs to a new Zenodo deposition or an existing one (see Zenodo Setup for the access token).

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zenodo_token=/path/to/zenodo/token/file    # file holding your Zenodo access token

cartloader upload_zenodo \
  --in-dir ./cartload2 \
  --upload-method catalog \
  --zenodo-token ${zenodo_token} \
  --title "Your Title" \
  --creators "Lastname, Firstname" \
  --description "This is an example description"
Parameter Required Type Description
--in-dir required string Directory with the CartLoader packaging output
--zenodo-token required string Path to the file holding your Zenodo access token
--upload-method string Which files to upload: all (every file in --in-dir; default), catalog (the files listed in catalog.yaml), or files (the names given with --files)
--catalog-yaml string Catalog to read with --upload-method catalog (default: <in-dir>/catalog.yaml)
--zenodo-deposition-id string Existing deposition to upload into (default: create a new one)
--title required 1 string Title of the deposition
--creators required 1 list of str Creators in "Lastname, Firstname" format, each quoted
--description string Description of the deposition

1: Required when creating a new deposition, or when the existing one lacks it.

Output Data

See output details in the reference pages for run_ficture2 and run_cartload2.