2026-10-13T20:41:55Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33813763 2026-09-15T17:52:51Z category_146 category_272 category_734 category_931 category_69 category_106 category_133 portal_5 item_type_3 month_year_09_2026

<p>Representative software tools for spatial transcriptomics analysis, with supported analyses, a representative citation, and indicative strengths and limitations to aid selection. Tools are examples, not endorsements, and several alternatives exist for each task. Maintenance status, software versions, and current capabilities should be verified (e.g., on the project repository) at the time of use.</p> Nagomi Kurogi (24949858) Koki Shimbara (24949861) Tatsuya Koreeda (24949864) Koki Tsuyuzaki (6323219) Space Science Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified Information Systems not elsewhere classified Inorganic Chemistry Science Policy Plant Biology ten quick tips serial tissue sections review provides biologists leveraging public datasets integrating complementary modalities highlight current limitations g ., merfish et al </ dimensional tissue architecture given biological question g ., visium cell rna sequencing whether st suits div >< p process st data visium hd spanning sequencing data structures biological context study objectives spatial transcriptomics spatial proteomics software tools sharing results reconstructing three neutral roadmap incorporating st foundational work experimental design expanded rapidly enables genome cosmx smi computational tools <p>Representative software tools for spatial transcriptomics analysis, with supported analyses, a representative citation, and indicative strengths and limitations to aid selection. Tools are examples, not endorsements, and several alternatives exist for each task. Maintenance status, software versions, and current capabilities should be verified (e.g., on the project repository) at the time of use.</p> 2026-09-15T17:52:44Z Dataset Dataset 10.1371/journal.pcbi.1014757.t002 https://figshare.com/articles/dataset/_p_Representative_software_tools_for_spatial_transcriptomics_analysis_with_supported_analyses_a_representative_citation_and_indicative_strengths_and_limitations_to_aid_selection_Tools_are_examples_not_endorsements_and_several_alternatives_e/33813763 CC BY 4.0