Seq-Scope Starter Tutorial

Input Data

This tutorial uses an example SGE from mouse hippocampus, extracted via spatial masking from a Seq-Scope coronal brain slice.

File Format

Actual input formats are platform-dependent. Please refer to the Vignettes for detailed input specifications by each platform.

SeqScope provides SGE with three files:

barcodes.tsv.gz – spatial barcode metadata

AAAACAAAAACCTTCTTCGGACACTGGTCT  1   20  1   1   295288  1422349 0,1,0,0,0
AAAACAAAAATCCTGTTATACATGCCATGG  2   45  1   1   1745544 1110720 2,2,1,0,1
AAAACAAAACACGGGAAAAAACTATAGGTG  3   58  1   1   887244  250820  7,7,5,0,1

• Column 1: Sorted spatial barcodes
• Column 2: 1-based integer index of spatial barcodes, used in matrix.mtx.gz
• Column 3: 1-based integer index from the full barcode that is in the STARsolo output
• Column 4: Lane ID (fixed as 1)
• Column 5: Tile ID (fixed as 1)
• Column 6: X-coordinates
• Column 7: Y-coordinates
• Column 8: Five comma-separated numbers denote the count per spatial barcode for "Gene", "GeneFull", "Spliced", "Unspliced", and "Ambiguous".

features.tsv.gz – feature metadata

ENSMUSG00000100764  Gm29155 1   1,1,1,0,0
ENSMUSG00000100635  Gm29157 2   0,0,0,0,0
ENSMUSG00000100480  Gm29156 3   0,0,0,0,0

• Column 1: Feature ID
• Column 2: Feature symbol
• Column 3: 1-based integer index of genes, used in matrix.mtx.gz
• Column 4: Five comma-separated numbers denote the count per gene "Gene", "GeneFull", "Spliced", "Unspliced", and "Ambiguous".

matrix.mtx.gz – expression count matrix

%%MatrixMarket matrix coordinate integer general
%
33989 2928173 5404336
2487 1 0 1 0 0 0
5104 2 1 1 0 0 1

• Header: Initial lines form the header, declaring the matrix's adherence to the Market Matrix (MTX) format, outlining its traits. This may include comments (lines beginning with %) for extra metadata, all marked by a “%”.
• Dimensions: Following the header, the first line details the matrix dimensions: the count of rows (features), columns (barcodes), and non-zero entries.
• Data Entries: After the dimensions, subsequent lines enumerate non‑zero entries in seven columns: row index (feature index), column index (barcode index), and five values (expression levels) corresponding to "Gene", "GeneFull", "Spliced", "Unspliced", and "Ambiguous".
  • "Gene": represents unique, confidently mapped transcript count ("gene name"-based);
  • "GeneFull": denotes total transcript count assigned to gene (includes ambiguities).

Data Access

The example data is hosted on Zenodo (10.5281/zenodo.17953582).

Follow the commands below to download the example data.

work_dir=/path/to/work/directory
cd $work_dir
wget  https://zenodo.org/records/17953582/files/seqscope_starter.raw.tar.gz 
tar -zxvf seqscope_starter.raw.tar.gz 

Set Up the Environment

Pre-installed tools

Please ensure you have installed all required tools (See Installation).

Define paths to all required binaries and resources. Optionally, specify a fixed color map for consistent rendering.

# ====
# Replace each placeholder with the actual path on your system.  
# ====

work_dir=/path/to/work/directory        # path to work directory that contains the downloaded input data
cd $work_dir

# Define paths to required binaries and resources
spatula=/path/to/spatula/binary         # path to spatula executable
punkst=/path/to/punkst/binary           # path to FICTURE2 (punkst) executable
tippecanoe=/path/to/tippecanoe/binary   # path to tippecanoe executable
pmtiles=/path/to/pmtiles/binary         # path to pmtiles executable
aws=/path/to/aws/cli/binary             # path to AWS CLI binary

# (Optional) Define path to color map. 
cmap=/path/to/color/map                 # Path to fixed color map. `CartLoader` includes one at cartloader/assets/fixed_color_map_256.tsv.

# Number of jobs
n_jobs=10                               # If not specified, the number of jobs defaults to 1.

# Activate the bioconda environment
conda activate ENV_NAME                 # replace ENV_NAME with your conda environment name

Define data ID and analysis parameters:

# Unique identifier for your dataset
DATA_ID="seqscope_hippo"                # change this to reflect your dataset name
PLATFORM="seqscope"                     # platform information
SCALE=1000                              # scale from coordinate to micrometer

# LDA parameters
train_width=18                           # 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 are applied)

How to Define Scaling Factors for Seq-Scope?

The latest SeqScope with an Illumina NovaSeq 6000 uses NovaScope pipeline to process sequencing data. NovaScope defaults to generate SGE at nanometer (nm) resolution, meaning each pixel corresponds to 1 nm.

Thus, use 1000 as scaling factor from coordinate to micrometer since 1000 nm = 1 µm.

SGE Format Conversion

Convert the raw input to the unified SGE format. See more details in SGE Format Conversion.

cartloader sge_convert \
  --makefn sge_convert.mk \
  --platform ${PLATFORM} \
  --in-mex ./raw \
  --units-per-um ${SCALE} \
  --out-dir ./sge \
  --exclude-feature-regex '^(BLANK|NegCon|NegPrb)' \
  --sge-visual \
  --spatula ${spatula} \
  --n-jobs ${n_jobs}

Parameter	Required	Type	Description
--platform	required	string	Platform (options: 10x_visium_hd, seqscope, 10x_xenium, bgi_stereoseq, cosmx_smi, vizgen_merscope, pixel_seq, generic)
--in-mex	required	string	Path to the input MEX directory containing gene × barcode matrix
--units-per-um	required	float	Scale to convert coordinates to microns (default: 1.0)
--out-dir	required	string	Output directory for the converted SGE files
--makefn		string	File name for the generated Makefile (default: sge_convert.mk)
--exclude-feature-regex		regex	Pattern to exclude control features
--sge-visual		flag	Enable SGE visualization step (generates a diagnostic image) (default: false)
--spatula		string	Path to the spatula binary (default: spatula)
--n-jobs		int	Number of parallel jobs for processing (default: 1)

FICTURE Analysis

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

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 \
  --cmap-file ${cmap} \
  --exclude-feature-regex '^(mt-.*$|Gm\d+$)' \
  --out-dir ./ficture2 \
  --width ${train_width} \
  --n-factor ${n_factor} \
  --spatula ${spatula} \
  --ficture2 ${punkst} \
  --n-jobs ${n_jobs} \
  --threads ${n_jobs}

Parameter	Required	Type	Description
--main	required 1	flag	Enable CartLoader to run all five steps
--in-transcript	required	string	Path to input transcript-level SGE file
--out-dir	required	string	Path to output directory
--width	required	int or comma-separated list	LDA training hexagon width(s)
--n-factor	required	int or comma-separated list	Number of LDA factors
--makefn		string	File name for the generated Makefile (default: run_ficture2.mk )
--in-feature		string	Path to input feature file
--in-minmax		string	Path to input coordinate min/max file
--cmap-file		string	Path to color map file
--exclude-feature-regex		regex	Pattern to exclude features
--spatula		string	Path to the spatula binary (default: spatula)
--ficture2		string	Path to the punkst directory (defaults to punkst repository within submodules directory of CartLoader)
--n-jobs		int	Number of parallel jobs (default: 1)
--threads		int	Number of threads per job (default: 1)

_{¹: CartLoader requires the user to specify at least one action. Available actions includes: --tile to run tiling step; --segment to run segmentation step; --init-lda to run LDA training step; --decode to run decoding step; --summary to run summarization step; --main to run all above five actions.}

CartLoader Asset Packaging

Generate pmtiles and web-compatible tile directories. See more details in Reference page.

# Example A: With FICTURE outputs (integrates factors + joins)
cartloader run_cartload2 \
  --makefn run_cartload2.mk \
  --fic-dir ./ficture2 \
  --out-dir ./cartload2 \
  --id ${DATA_ID} \
  --spatula ${spatula} \
  --pmtiles ${pmtiles} \
  --tippecanoe ${tippecanoe} \
  --n-jobs ${n_jobs} \
  --threads ${n_jobs}

# Example B: SGE-only (package molecules without FICTURE)
cartloader run_cartload2 \
  --makefn run_cartload2.mk \
  --sge-dir ./sge_convert \
  --out-dir ./cartload2 \
  --id ${DATA_ID} \
  --spatula ${spatula} \
  --pmtiles ${pmtiles} \
  --tippecanoe ${tippecanoe} \
  --n-jobs ${n_jobs} \
  --threads ${n_jobs}

Parameter	Required	Type	Description
--out-dir	required	string	Path to the output directory for PMTiles and web tiles
--id	required	string	Dataset ID used for naming outputs and metadata
--fic-dir		string	Path to FICTURE outputs (enables factor layers + molecule–factor joins)
--sge-dir		string	Path to SGE outputs from sge_convert (enables SGE-only packaging)
--in-sge-assets		string	File name of SGE assets JSON/YAML in --sge-dir (default: sge_assets.json)
--in-fic-params		string	File name of FICTURE params JSON/YAML in --fic-dir (default: ficture.params.json)
--makefn		string	File name for the generated Makefile (default: run_cartload2.mk)
--spatula		string	Path to the spatula binary (default: spatula)
--pmtiles		string	Path to the pmtiles binary (default: pmtiles)
--tippecanoe		string	Path to the tippecanoe binary (default: tippecanoe)
--n-jobs		int	Number of parallel jobs (default: 1)
--threads		int	Number of threads per job (default: 4)

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.

AWS Uploads

Upload the generated CartLoader outputs to your designated AWS S3 directory:

# AWS S3 target location for cartostore
S3_DIR=/s3/path/to/s3/dir              # Recommend to use DATA_ID as directory name, such as s3://bucket_name/xenium-v1-humanlung-cancer-ffpe

cartloader upload_aws \
  --in-dir ./cartload2 \
  --s3-dir "${S3_DIR}" \
  --aws ${aws} \
  --n-jobs ${n_jobs}

Parameter	Required	Type	Description
--in-dir	required	string	Path to the input directory containing the CartLoader asset packaging output
--s3-dir	required	string	Path to the target S3 directory for uploading
--aws		string	Path to the AWS CLI binary
--n-jobs		int	Number of parallel jobs

Zenodo Uploads

Upload the generated CartLoader outputs to your designated Zenodo deposition or a new deposition.

zenodo_token=/path/to/zenodo/token/file    # replace /path/to/zenodo/token/file by path to your zenodo token file

cartloader upload_zenodo \
  --in-dir ./cartload2 \
  --upload-method catalog \
  --zenodo-token $zenodo_token \
  --title  "Your Title" \
  --creators "Your Name" \
  --description "This is an example description"

Parameter	Required	Type	Description
--in-dir	required	string	Path to the input directory containing the CartLoader asset packaging output
--upload-method	required	string	Method to determine which files to upload. Options: all to upload all files in --in-dir; catalog to upload files listed in a catalog YAML file; user_list to upload files explicitly listed via --in-list
--catalog-yaml		string	Required if --upload-method catalog. Path to catalog.yaml generated in run_cartload2. If absent, uses the catalog in the input directory specified by --in-dir.
--zenodo-token	required	string	Path to your Zenodo access token file
--title	required	string	Required when creating a new deposition (i.e., if --zenodo-deposition-id is omitted). Title for the new Zenodo deposition.
--creators	required	list of str	List of creators in "Lastname, Firstname" format.

Output Data

• 

  ---

  View/Explore

  The output are available in both CartoScope and Zenodo.

  Explore in CartoScope

  Download from Zenodo

See more details of output at the Reference pages for run_ficture2 and run_cartload2.