{"doi":"10.1101/2023.09.03.556122","title":"Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning","abstract":"Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually-tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep learning models for cell segmentation and spot detection with a probabilistic gene decoder to quantify single-cell gene expression accurately. Polaris offers a unifying, turnkey solution for analyzing spatial transcriptomics data from MERFSIH, seqFISH, or ISS experiments. Polaris is available through the DeepCell software library (https://github.com/vanvalenlab/deepcell-spots) and https://www.deepcell.org.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":392581,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.946,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":51120,"name":"Xuefei Wang","orcid":"0000-0002-9327-9543","position":1,"is_corresponding":false},{"id":1166171,"name":"Nitzan Razin","orcid":"0000-0001-7571-5658","position":2,"is_corresponding":false},{"id":1166604,"name":"Tom Dougherty","orcid":null,"position":3,"is_corresponding":false},{"id":616342,"name":"Rosalind J. Xu","orcid":"0000-0002-4423-893X","position":4,"is_corresponding":false},{"id":1159871,"name":"Lincoln Ombelets","orcid":"0000-0002-5625-5411","position":5,"is_corresponding":false},{"id":1160503,"name":"Edward Pao","orcid":null,"position":6,"is_corresponding":false},{"id":233127,"name":"William D. Graf","orcid":"0000-0002-4264-9479","position":7,"is_corresponding":false},{"id":97970,"name":"Jeffrey R. Moffitt","orcid":"0000-0002-3836-3101","position":8,"is_corresponding":false},{"id":692532,"name":"Yisong Yue","orcid":"0000-0001-9127-1989","position":9,"is_corresponding":false},{"id":37873,"name":"David Van Valen","orcid":"0000-0001-7534-7621","position":10,"is_corresponding":false},{"id":1159661,"name":"Emily Laubscher","orcid":"0009-0008-0242-0507","position":0,"is_corresponding":true}],"reference_count":38,"raw_metadata":null,"created_at":"2026-07-19T01:18:56.730121Z","pmid":"37732188","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}