{"doi":"10.1038/s41592-024-02404-5","title":"Arkitekt: streaming analysis and real-time workflows for microscopy","abstract":null,"journal":"Nature Methods","year":2024,"id":643446,"datarank":0.37273599746820013,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.0,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1314066,"name":"Stéphane Bancelin","orcid":"0000-0001-6328-0423","position":1,"is_corresponding":false},{"id":1674207,"name":"Tom Delaire","orcid":null,"position":2,"is_corresponding":false},{"id":1674208,"name":"Alexander Wilhelmi","orcid":"0000-0002-4766-5128","position":3,"is_corresponding":false},{"id":578508,"name":"Florian Levet","orcid":"0000-0002-4009-6225","position":4,"is_corresponding":false},{"id":1038463,"name":"Maren Engelhardt","orcid":"0000-0001-8020-6604","position":5,"is_corresponding":false},{"id":636969,"name":"Virgile Viasnoff","orcid":"0000-0003-3949-2244","position":6,"is_corresponding":false},{"id":1674209,"name":"Rémi Galland","orcid":"0000-0001-7117-3281","position":7,"is_corresponding":false},{"id":839786,"name":"U. Valentin Nägerl","orcid":"0000-0001-6831-9008","position":8,"is_corresponding":false},{"id":578510,"name":"Jean‐Baptiste Sibarita","orcid":"0000-0002-9920-7700","position":9,"is_corresponding":false},{"id":1166019,"name":"Johannes Roos","orcid":"0000-0001-7409-9101","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Arkitekt: streaming analysis and real-time workflows for microscopy","abstract":"Quantitative microscopy workflows have evolved dramatically over the past years, progressively becoming more complex with the emergence of deep learning. Long-standing challenges such as three-dimensional segmentation of complex microscopy data can finally be addressed, and new imaging modalities are breaking records in both resolution and acquisition speed, generating gigabytes if not terabytes of data per day. With this shift in bioimage workflows comes an increasing need for efficient orchestration and data management, necessitating multitool interoperability and the ability to span dedicated computing resources. However, existing solutions are still limited in their flexibility and scalability and are usually restricted to offline analysis. Here we introduce Arkitekt, an open-source middleman between users and bioimage apps that enables complex quantitative microscopy workflows in real time. It allows the orchestration of popular bioimage software locally or remotely in a reliable and efficient manner. It includes visualization and analysis modules, but also mechanisms to execute source code and pilot acquisition software, making 'smart microscopy' a reality.","is_dataset_classified":null,"base_score":2.3978952727983707,"endowment":2.3978952727983707,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39294366","pmcid":null,"openalex_id":"https://openalex.org/W4402623571","authors":[],"funders":[{"funder_name":"European Commission","grant_id":"794492","title":"In vivo super-resolution imaging of synapses in the hippocampus"}],"total_grants":1,"fwci":4.4256,"citation_percentile":0.93919638,"influential_citations":0,"citation_trend":[{"year":2024,"count":1},{"year":2025,"count":6},{"year":2026,"count":3}],"oa_status":"green","license":"Springer Nature TDM","oa_locations":[{"url":"https://hal.science/hal-04735193/document","host_type":"repository"},{"url":"https://hal.science/hal-04735193/document","host_type":"repository"},{"url":"https://www.nature.com/articles/s41592-024-02404-5.pdf","host_type":"publisher"},{"url":"https://www.nature.com/articles/s41592-024-02404-5","host_type":"publisher"},{"url":"https://hal.science/hal-04735193","host_type":"repository"},{"url":"https://doi.org/10.1038/s41592-024-02404-5","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39294366","host_type":"repository"},{"url":"https://hal.science/hal-04735193v1/document","host_type":""},{"url":"https://hal.science/hal-04735193v1","host_type":""}],"fields_of_study":["Cell Image Analysis Techniques","Single-cell and spatial transcriptomics","Scientific Computing and Data Management","0202 electrical engineering, electronic engineering, information engineering","02 engineering and technology","Workflow","Microscopy","Software","Image Processing, Computer-Assisted","Humans"],"mesh_terms":["Humans","Image Processing, Computer-Assisted","Microscopy","Software","Workflow"],"keywords":["Computer science","Workflow","Orchestration","Interoperability","Scalability","Flexibility (engineering)","Visualization","Software","Artificial intelligence","Database","World Wide Web","Operating system","Microscopy","Image Processing, Computer-Assisted","Humans","[INFO] Computer Science [cs]","[PHYS] Physics [physics]"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-08T17:01:44.323058Z","pmid":null,"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":[]}