{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/hest-1k-a-dataset-for-spatial-transcriptomics","title":"HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis","arxiv_id":"2406.16192","date":"2024-06-23","proceeding":null,"authors":["Guillaume Jaume","Paul Doucet","Andrew H. Song","Ming Y. Lu","Cristina Almagro-Pérez","Sophia J. Wagner","Anurag J. Vaidya","Richard J. Chen","Drew F. K. Williamson","Ahrong Kim","Faisal Mahmood"],"abstract":"Spatial transcriptomics enables interrogating the molecular composition of tissue with ever-increasing resolution and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology, as reflected by H&E-stained whole slide images (WSIs), encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,229 spatial transcriptomic profiles, each linked to a WSI and extensive metadata. HEST-1k was assembled from 153 public and internal cohorts encompassing 26 organs, two species (Homo Sapiens and Mus Musculus), and 367 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 2.1 million expression--morphology pairs and over 76 million nuclei. To support its development, we additionally introduce the HEST-Library, a Python package designed to perform a range of actions with HEST samples. We test HEST-1k and Library on three use cases: (1) benchmarking foundation models for pathology (HEST-Benchmark), (2) biomarker exploration, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed at https://github.com/mahmoodlab/hest.","url_abs":"https://arxiv.org/abs/2406.16192v2","url_pdf":"https://arxiv.org/pdf/2406.16192v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"hest-1k-a-dataset-for-spatial-transcriptomics","repo_url":"https://github.com/mahmoodlab/hest","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"representation-learning","task_name":"Representation Learning"},{"task_slug":"whole-slide-images","task_name":"whole slide images"}],"methods":[{"method_slug":null,"method_name":"Library"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2406.16192","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2406.16192"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"deterministic:regex_extraction","url":"https://github.com/mahmoodlab/hest","reach":null}],"summary":{"ran_draft_wrong":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":1,"samples":[{"code_sha256_prefix":"469cbfd300c7b3ba","entry":"get_path","repo":"mahmoodlab/hest","repo_kind":"official","path":"src/hest/bench/benchmark.py","file_url":"https://github.com/mahmoodlab/hest/blob/HEAD/src/hest/bench/benchmark.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"469cbfd300c7b3ba"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}