{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:03:35Z","timestamp":1761059015343},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing 3D-FISH microscopy images is Smart 3D-FISH, an ImageJ plug-in designed to automatically analyze distances between genes. One of the drawbacks of Smart 3D-FISH is that it has a rather basic user interface and produces its results in various text and image files thus making the data post-processing step time consuming. We developed a new Smart 3D-FISH graphical user interface, NEMO, which provides all information in the same place so that results can be checked and validated efficiently. NEMO gives users the ability to drive their experiments analysis in either automatic, semi-automatic or manual detection mode. We also tuned Smart 3D-FISH to better analyze chromosome territories.<\/jats:p>\n               <jats:p>Availability: NEMO is a stand-alone Java application available for Windows and Linux platforms. The program is distributed under the creative commons licence and can be freely downloaded from https:\/\/www-lgc.toulouse.inra.fr\/nemo<\/jats:p>\n               <jats:p>Contact: \u00a0eddie.iannuccelli@toulouse.inra.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq013","type":"journal-article","created":{"date-parts":[[2010,1,16]],"date-time":"2010-01-16T01:14:00Z","timestamp":1263604440000},"page":"696-697","source":"Crossref","is-referenced-by-count":64,"title":["NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments"],"prefix":"10.1093","volume":"26","author":[{"given":"E.","family":"Iannuccelli","sequence":"first","affiliation":[{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"}]},{"given":"F.","family":"Mompart","sequence":"additional","affiliation":[{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"}]},{"given":"J.","family":"Gellin","sequence":"additional","affiliation":[{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"}]},{"given":"Y.","family":"Lahbib-Mansais","sequence":"additional","affiliation":[{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"}]},{"given":"M.","family":"Yerle","sequence":"additional","affiliation":[{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"}]},{"given":"T.","family":"Boudier","sequence":"additional","affiliation":[{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"},{"name":"1 Institut National de la Recherche Agronomique, Laboratoire de G\u00e9n\u00e9tique Cellulaire, BP 52627, 31326 Castanet-Tolosan, 2 IFR83, Universit\u00e9 Pierre et Marie Curie, 7 Quai Saint Bernard and 3 Universit\u00e9 Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2010,1,14]]},"reference":[{"key":"2023012511004993300_B1","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1002\/cyto.a.20170","article-title":"Smart 3D-FISH: automation of distance analysis in nuclei of interphase cells by image processing","volume":"67","author":"Gue","year":"2005","journal-title":"Cytometry A"},{"key":"2023012511004993300_B2","volume-title":"ImageJ, U.S. National Institutes of Health","author":"Rasband","year":"1997"},{"key":"2023012511004993300_B3","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1006\/excr.2002.5513","article-title":"Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH)","volume":"276","author":"Solovei","year":"2002","journal-title":"Exp. Cell Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/5\/696\/48860345\/bioinformatics_26_5_696.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/5\/696\/48860345\/bioinformatics_26_5_696.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:04:58Z","timestamp":1674644698000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/5\/696\/212832"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1,14]]},"references-count":3,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2010,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq013","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,3,1]]},"published":{"date-parts":[[2010,1,14]]}}}