{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T06:57:53Z","timestamp":1777705073984,"version":"3.51.4"},"reference-count":70,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":46,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Quant. Biol."],"published-print":{"date-parts":[[2023,9]]},"abstract":"<jats:sec><jats:label\/><jats:p>In this review, we introduced five different multiplex FISH methods used for image\u2010based spatial multi\u2010omics: seqFISH+, merFISH, DNA seqFISH+, DNA merFISH, and MINA. We provided a systematic collective perspective to review these FISH methods that could significantly benefit researchers on conducting their studies in the field. Our study provided an informative survey on these multiplex FISH methods. Therefore, this review would provide better understanding for researchers in the community to help them select the proper method, in order to understand the molecular mechanism in life sciences.<\/jats:p><\/jats:sec><jats:sec><jats:title>Background<\/jats:title><jats:p>Spatial multi\u2010omics are demonstrated to be a powerful method to assist researchers on genetic studies. In this review, bioimaging\u2010based spatial multi\u2010omics techniques such as seqFISH+, merFISH, integrated DNA seqFISH+, DNA merFISH, and MINA are introduced along with each technique\u2019s probe design, development, and imaging processes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>seqFISH employed 4\u20135 fluorophores to barcode and conducted multiple rounds of hybridization, in order that mRNA can be identified through color\u2010coding. seqFISH+ added 60 pseudo\u2010color and distributed them equally into three channels to enhance imaging power, in order that <jats:italic>i.e.<\/jats:italic>, 24,000 genes can be imaged in total. merFISH utilized 4 out 16 Hamming distance to innovatively provide a robust error\u2010detecting method. MINA, a methodology combining merFISH (multiplexed error\u2010robust fluorescence <jats:italic>in situ<\/jats:italic> hybridization) and chromosomal tracing, enabled multiplexed genomic architecture imaged in mammalian single cells. Optical reconstruction of chromatin architecture (ORCA) a method that could conduct DNA path tracing in nanoscale manner with kilobase resolution, an FISH variation that improved genetic resolution, enable high\u2010precision fiducial registration and sequential imaging, and utilized Oligopaint probe to hybridize the short genomic region ranging from 2 to 10 kilobase. ORCA then prescribes these short section primary probes with individual barcodes to attach fluorophore and to be imaged.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>This review concentrated on providing a comprehensive overview for these spatial\u2010multi\u2010omics techniques with the intention on helping researchers on selecting appropriate technique for their research.<\/jats:p><\/jats:sec>","DOI":"10.15302\/j-qb-023-0332","type":"journal-article","created":{"date-parts":[[2023,7,21]],"date-time":"2023-07-21T02:45:22Z","timestamp":1689907522000},"page":"231-245","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Introduction to bioimaging\u2010based spatial multi\u2010omic novel methods"],"prefix":"10.1002","volume":"11","author":[{"given":"Yan","family":"Yan","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics Tsinghua University  Beijing 100084 China"},{"name":"Center for Synthetic &amp; Systems Biology Tsinghua University  Beijing 100084 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liheng","family":"Yang","sequence":"additional","affiliation":[{"name":"Seaver College Pepperdine University  Malibu CA 90263 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leyuan","family":"Meng","sequence":"additional","affiliation":[{"name":"College of Animal Sciences Heping campus Jilin University  Jilin 130062 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haochen","family":"Su","sequence":"additional","affiliation":[{"name":"Sidney Sussex College  Sidney Street Cambridge CB2 3HU United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology Nanfang Hospital Southern Medical University  Guangzhou 510515 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Le","family":"Yu","sequence":"additional","affiliation":[{"name":"Foshan Protogene Tech. 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