rctd-py

Spatial transcriptomics deconvolution — 4–41x faster than R spacexr with GPU

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A Python reimplementation of the spacexr RCTD algorithm (Cable et al., Nature Biotechnology 2022) with GPU acceleration via PyTorch.

Deconvolve spatial transcriptomics spots (Visium, Xenium, MERFISH, Slide-seq, …) into cell type proportions using a scRNA-seq reference — in minutes instead of hours.

✨ Highlights

⚡ 4–41x faster than R spacexr	Xenium 58k cells, multi mode: 3.7 min vs 2.6 hours in R
🎯 99.7% concordance with R spacexr	100% with sigma_override — per-pixel solver is bit-identical
🔧 Drop-in replacement	Same algorithm, same parameters, same results — just faster
📦 pip install rctd-py	Pure Python, works on CPU out of the box

Benchmarks

Benchmarked on 3 datasets across all RCTD modes (full, doublet, multi). All runs on AMD EPYC 9554 nodes (128 cores, 1.15 TB RAM). GPU: NVIDIA RTX PRO 6000 Blackwell (96 GB VRAM) on the same node class. CPU rctd-py: device="cpu", 8 threads (OMP_NUM_THREADS=8). R spacexr: 8 CPU cores (doParallel). All rctd-py timings use warm torch.compile cache.

Runtime comparison (all modes)

Dataset	Cells	K	Mode	R spacexr	rctd-py GPU	GPU vs R
Xenium Liver (small)	13,940	45	full	5.3 min	1.4 min	3.8x
			doublet	14.1 min	1.5 min	9.4x
			multi	6.7 min	1.6 min	4.2x
Xenium Mouse Brain	36,362	22	full	4.7 min	0.8 min	5.9x
			doublet	12.4 min	0.9 min	13.8x
			multi	9.5 min	1.1 min	8.6x
Xenium Liver (large)	58,191	45	full	14.3 min	3.6 min	4.0x
			doublet	51.1 min	3.7 min	13.8x
			multi	153.3 min	3.7 min	41.4x
VisiumHD Mouse Brain (8µm)	392,580	22	full	—	1.0 min	—

GPU timings include sigma estimation (25–53s depending on dataset). The VisiumHD benchmark demonstrates scalability to ~400k spots in about a minute (33s deconv + 25s sigma, Blackwell GPU). GPU speedup is highest in doublet mode (9–14x) and multi mode on large datasets (41x for Region 3) because R spacexr's pairwise fitting and greedy selection are the main bottlenecks — rctd-py batches all C(K,2) pairs into a single tensor operation.

Memory requirements

Dataset	Cells	K	Peak VRAM	Peak RSS
Xenium Liver (small)	13,940	45	2.6 GB	34 GB
Xenium Mouse Brain	36,362	22	2.6 GB	5 GB
Xenium Liver (large)	58,191	45	2.6 GB	34 GB
VisiumHD Mouse Brain (8µm)	392,580	22	41 GB	47 GB

Peak VRAM for Xenium-scale datasets is ~2.6 GB (doublet mode, default batch size). VisiumHD at 392k spots uses 41 GB VRAM with auto batch sizing (200k spots per batch). RSS is dominated by the reference matrix and scales with K and N. Use the batch_size parameter to control peak VRAM — smaller batches trade throughput for lower memory.

Note: The main speedup comes from PyTorch's vectorized batched solver. GPU rctd-py times are nearly identical across modes (~2–7 min) while R spacexr times vary 3–10x between modes, because rctd-py batches pairwise/iterative fits into tensor operations that scale efficiently. The GPU advantage is largest for smaller cell type panels (K < 25) where GPU eigendecomposition handles all pairwise fits on-device.

Quick Start

from rctd import Reference, run_rctd
import anndata

# Load data
reference = Reference(anndata.read_h5ad("reference.h5ad"), cell_type_col="cell_type")
spatial = anndata.read_h5ad("spatial.h5ad")

# Run RCTD — handles normalization, sigma estimation, and deconvolution
result = run_rctd(spatial, reference, mode="doublet")

📓 Tutorial notebook (marimo) · 🌐 Rendered tutorial

Command Line

After installation, the rctd command is available with three subcommands:

# Check environment, versions, and GPU availability
rctd info
rctd info --json          # machine-readable output

# Validate inputs before a long run (fast, no GPU needed)
rctd validate spatial.h5ad reference.h5ad
rctd validate spatial.h5ad reference.h5ad --json

# Run deconvolution (default: doublet mode)
rctd run spatial.h5ad reference.h5ad
rctd run spatial.h5ad reference.h5ad --mode full
rctd run spatial.h5ad reference.h5ad --mode multi

# Common options
rctd run spatial.h5ad reference.h5ad \
    --mode doublet \
    --output results.h5ad \
    --device cuda \
    --batch-size 5000 \
    --umi-min 20 \
    --cell-type-col cell_type \
    --sigma-override 63

# JSON output for pipelines / AI agents
rctd run spatial.h5ad reference.h5ad --json --quiet

Output format

Results are written into a copy of the input spatial h5ad. Default output path is <spatial_stem>_rctd.h5ad.

Slot	Content	Modes
.obsm["rctd_weights"]	Cell type weights (N x K)	all
.obs["rctd_dominant_type"]	Top cell type per pixel	all
.obs["rctd_spot_class"]	singlet / doublet_certain / doublet_uncertain / reject	doublet
.obs["rctd_first_type"]	Primary cell type	doublet
.obs["rctd_second_type"]	Secondary cell type	doublet
.obsm["rctd_weights_doublet"]	Doublet weights (N x 2)	doublet
.obs["rctd_converged"]	Convergence flag	full
.obs["rctd_n_types"]	Number of types per pixel	multi
.obsm["rctd_sub_weights"]	Per-selected-type weights	multi
.obsm["rctd_cell_type_indices"]	Selected type indices	multi
.uns["rctd_mode"]	Mode used	all
.uns["rctd_config"]	Full config dict	all
.uns["rctd_cell_type_names"]	Cell type name list	all

Filtered pixels (below --umi-min) have NaN weights and "filtered" labels.

All rctd run options

Option	Default	Description
--mode	doublet	full, doublet, or multi
--output / -o	<stem>_rctd.h5ad	Output path
--device	auto	auto, cpu, or cuda
--batch-size	10000	GPU batch size (lower = less VRAM)
--cell-type-col	cell_type	Reference obs column for cell types
--sigma-override	(auto)	Skip sigma estimation, use this value
--umi-min	100	Minimum UMI per pixel
--umi-max	20000000	Maximum UMI per pixel
--json	off	Print JSON summary to stdout
--quiet / -q	off	Suppress progress messages
--dtype	float64	float32 or float64
--gene-cutoff	0.000125	Bulk gene expression threshold
--fc-cutoff	0.5	Bulk fold-change threshold
--gene-cutoff-reg	0.0002	Reg gene expression threshold
--fc-cutoff-reg	0.75	Reg fold-change threshold
--max-multi-types	4	Max types per pixel (multi mode)
--confidence-threshold	5.0	Singlet confidence threshold
--doublet-threshold	20.0	Doublet certainty threshold
--cell-min	25	Min cells per type in reference
--n-max-cells	10000	Max cells per type (downsampling)
--min-umi-ref	100	Min UMI for reference cells

Installation

uv pip install rctd-py   # or: pip install rctd-py

GPU setup and CUDA compatibility

Recommended setup

Install PyTorch with CUDA before installing rctd-py — pip install rctd-py alone pulls CPU-only PyTorch on most systems:

# CUDA 12.4 (recommended for drivers >= 550.54)
uv pip install torch --index-url https://download.pytorch.org/whl/cu124
uv pip install rctd-py

# CUDA 12.1 (for older drivers >= 530.30)
uv pip install torch --index-url https://download.pytorch.org/whl/cu121

# CUDA 11.8 (legacy, drivers >= 520.61)
uv pip install torch --index-url https://download.pytorch.org/whl/cu118

Verify GPU detection

import torch
print(torch.cuda.is_available())    # True  (False means CPU-only torch or driver issue)
print(torch.cuda.get_device_name()) # e.g. 'NVIDIA L40S'
print(torch.version.cuda)           # e.g. '12.4'

CUDA compatibility table

No separate CUDA toolkit installation needed. PyTorch ships its own CUDA runtime — you only need a compatible NVIDIA driver.

PyTorch version	Bundled CUDA	Minimum NVIDIA driver
2.5+	CUDA 12.4	>= 550.54
2.3–2.4	CUDA 12.1	>= 530.30
2.0–2.2	CUDA 11.8	>= 520.61

Tip: Check your driver version with nvidia-smi (top right of the output). This is the driver version, not the CUDA toolkit version — nvcc --version shows the toolkit version, which is irrelevant here since PyTorch bundles its own runtime.

Tested GPUs

GPU	VRAM	Speedup vs R (doublet)
NVIDIA RTX PRO 6000 Blackwell	96 GB	6–11x (see benchmarks above)
NVIDIA L40S	48 GB	4.2x (K=45, 14k cells)

Memory management

Peak VRAM scales with batch_size * K^2. Use the batch_size parameter to control GPU memory:

Available VRAM	Recommended batch_size	Peak VRAM (K=45)
24+ GB	10,000 (default)	~4 GB
8–16 GB	5,000	~2 GB
< 8 GB	2,000	~1 GB

Peak CPU RAM (RSS) is typically 2–3x peak VRAM, dominated by intermediate arrays.

Deconvolution Modes

Mode	What it does	Best for
full	Estimates weights for all K cell types per pixel (constrained IRWLS)	Visium, continuous mixtures
doublet	Classifies each pixel as singlet or doublet, estimates top 1–2 types	Slide-seq, sparse spatial
multi	Greedy forward selection of up to 4 cell types per pixel	Xenium, MERFISH, dense platforms

Validation

Validated against R spacexr on two Xenium liver datasets (45 cell types, 380 genes, doublet mode, UMI_min=20):

Dataset	# cells	Dominant type agreement	With sigma_override
Xenium Liver (small)	13,940	99.73%	100%
Xenium Liver (large)	58,191	99.71%	—

The tiny default gap (0.27%) traces entirely to platform-effect estimation (fit_bulk), not the per-pixel solver — which is bit-identical to R. All disagreeing pixels are genuinely ambiguous (margin < 0.05 between top two types).

sigma_override is not needed for normal use. The default Python-estimated sigma is valid and produces near-identical results. It exists for specific scenarios:

• Validation — proving solver equivalence with R
• Migration — replicating exact R spacexr results when you already have R's sigma
• Reproducibility — locking sigma to a known value across runs

# Only if you need exact R concordance and know R's sigma value:
result = run_rctd(spatial, reference, mode="doublet", sigma_override=63)

Migrating from R spacexr

Parameter correspondence table

All defaults match R spacexr, so default R results reproduce with default rctd-py parameters.

Reference construction

R spacexr (Reference())	rctd-py (Reference())	Default	Description
cell_type_col (in meta.data)	cell_type_col	"cell_type"	Column name for cell type labels
CELL_MIN_INSTANCE	cell_min	25	Min cells per type to include
n_max_cells	n_max_cells	10000	Max cells per type (downsampled)
min_UMI	min_UMI	100	Min UMI for reference cells

RCTD configuration

R spacexr (create.RCTD())	rctd-py (RCTDConfig())	Default	Description
gene_cutoff	gene_cutoff	0.000125	Min normalized expression (bulk gene list)
fc_cutoff	fc_cutoff	0.5	Min log-FC (bulk gene list)
gene_cutoff_reg	gene_cutoff_reg	0.0002	Min normalized expression (DE gene list)
fc_cutoff_reg	fc_cutoff_reg	0.75	Min log-FC (DE gene list)
UMI_min	UMI_min	100	Min UMI per spatial pixel
UMI_max	UMI_max	20000000	Max UMI per spatial pixel
counts_MIN	counts_MIN	10	Min total counts for a gene
UMI_min_sigma	UMI_min_sigma	300	Min UMI for sigma estimation pixels
N_epoch	N_epoch	8	Epochs for platform effect estimation
N_fit	N_fit	100	Pixels sampled for sigma fitting
MIN_CHANGE_BULK	MIN_CHANGE_BULK	0.0001	Convergence threshold (bulk fitting)
MIN_CHANGE_REG	MIN_CHANGE_REG	0.001	Convergence threshold (per-pixel)
MIN_OBS	MIN_OBS	3	Min observations for DE gene selection
MAX_MULTI_TYPES	MAX_MULTI_TYPES	4	Max cell types per pixel (multi mode)
CONFIDENCE_THRESHOLD	CONFIDENCE_THRESHOLD	5.0	Singlet confidence threshold
DOUBLET_THRESHOLD	DOUBLET_THRESHOLD	20.0	Doublet certainty threshold
max_cores	N/A	—	See parallelism note below

rctd-py only (no R equivalent)

Parameter	Default	Description
max_iter	50	Max IRWLS iterations per pixel
step_size	0.3	IRWLS step size
K_val	1000	Spline discretization points
dtype	"float64"	"float32" saves GPU memory
device	"auto"	"cpu", "cuda", or "auto"

Parallelism

R spacexr uses max_cores to parallelize across pixels via doParallel. rctd-py uses vectorized PyTorch tensor operations instead — no max_cores parameter needed. For CPU thread control, set the OMP_NUM_THREADS environment variable before running:

export OMP_NUM_THREADS=8

For GPU acceleration, set device="cuda" in RCTDConfig() or pass --device cuda on the CLI.

API

Click to expand full API reference

run_rctd(spatial, reference, mode, config, batch_size, sigma_override)

End-to-end pipeline. Takes an AnnData spatial object and a Reference, returns a typed result (FullResult, DoubletResult, or MultiResult). Pass sigma_override (int) to skip sigma estimation and use a known value (e.g. from R).

Reference(adata, cell_type_col, cell_min, n_max_cells, min_UMI)

Constructs cell type profiles from a scRNA-seq AnnData. Filters cell types below cell_min, caps per-type cells at n_max_cells.

RCTD(spatial, reference, config)

Stateful class for step-by-step control. Call fit_platform_effects(), then run_full_mode, run_doublet_mode, or run_multi_mode.

RCTDConfig — key parameters

Parameter	Default	Description
UMI_min	100	Minimum UMI count per pixel
UMI_min_sigma	300	Minimum UMI for sigma estimation
N_fit	100	# pixels sampled for sigma fitting
MAX_MULTI_TYPES	4	Max cell types in multi mode
CONFIDENCE_THRESHOLD	5.0	Singlet confidence threshold
DOUBLET_THRESHOLD	20.0	Doublet certainty threshold
device	"auto"	"auto", "cpu", or "cuda" — force CPU/GPU

Result types

• FullResult — weights (N×K), cell_type_names, converged
• DoubletResult — weights, weights_doublet (N×2), spot_class, first_type, second_type
• MultiResult — weights, cell_type_indices, n_types, conf_list

Citation

If you use rctd-py, please cite the original RCTD paper:

@article{cable2022robust,
  title={Robust decomposition of cell type mixtures in spatial transcriptomics},
  author={Cable, Dylan M and Murray, Evan and Zou, Luli S and Goeva, Aleksandrina and Macosko, Evan Z and Chen, Fei and Bhatt, Shreya and Denber, Hannah S and others},
  journal={Nature Biotechnology},
  volume={40},
  pages={517--526},
  year={2022},
  doi={10.1038/s41587-021-00830-w}
}

Contributing

Contributions welcome! See CONTRIBUTING.md for setup instructions, or open an issue.

License

GNU General Public License v3.0