strandai

R client for the Strand AI Platform: upload H&E whole-slide images, run virtual multiplex-immunofluorescence inference (H&E → spatial proteomics), and download per-marker predictions as a SpatialExperiment or OME-Zarr/OME-TIFF. Functions use the strand_* prefix; the package is named strandai to avoid a clash with the unrelated strand package on CRAN.

📚 Full documentation: https://docs.strandai.com/sdks/r

Agent-readable API reference: https://app.strandai.com/docs/api.md · LLM index: https://app.strandai.com/llms.txt

Install

# From r-universe (recommended):
install.packages("strandai", repos = c("https://strand-ai.r-universe.dev", "https://cloud.r-project.org"))

# For SpatialExperiment results (recommended):
BiocManager::install("SpatialExperiment")

Quickstart

One blocking call runs the full pipeline — upload, submit, wait, download:

library(strandai)
client <- strand_client()  # reads STRAND_API_KEY

result <- strand_run(
  client, "biopsy.ome.tiff",
  markers = c("HER2", "CD8", "PD1"),
  output_dir = "./outputs/"
)
cat("Used", result$credits_used, "credits;",
    length(result$marker_outputs), "markers written\n")

Use the unified sample surface to browse owned and public slides, inspect an owned slide's job history, and update its attributes:

page <- strand_samples_list(client, scope = "all")
sample <- strand_samples_get(client, page$items[[1]]$id)

if (sample$ownership == "mine") {
  sample <- strand_patch_sample(
    client, sample$id,
    name = "Baseline biopsy",
    tags = c("baseline", "responding"),
    mpp = 0.26
  )
}

Price a prediction through the same operation that submits it:

estimate <- strand_predict(
  client, upload$id, c("CD8", "PanCK"), dry_run = TRUE
)

Uploads, model selection, async jobs, OME-TIFF export, and error handling are covered in the hosted docs.

Issues & support

File bug reports and feature requests at Strand-AI/strand-sdk-r/issues, or email support@strandai.com. This repository is a generated, read-only mirror of Strand AI's monorepo — pull requests opened here are overwritten by the next sync.

License

Apache 2.0