{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:57Z","timestamp":1740185097470,"version":"3.37.3"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2018,6,21]],"date-time":"2018-06-21T00:00:00Z","timestamp":1529539200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Portuguese Foundation for Science and Technology"},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006111","name":"MCTES","doi-asserted-by":"publisher","award":["SFRH\/BD\/88987\/2012"],"award-info":[{"award-number":["SFRH\/BD\/88987\/2012"]}],"id":[{"id":"10.13039\/501100006111","id-type":"DOI","asserted-by":"publisher"}]},{"name":"TUT Graduate Programme"},{"name":"Vilho, Yrjo and Kalle Vaisala Foundation"},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["295027","305342"],"award-info":[{"award-number":["295027","305342"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ASR"},{"name":"Jane & Aatos Erkko Foundation","award":["610536"],"award-info":[{"award-number":["610536"]}]},{"name":"ASR"},{"name":"FCT Strategic Program","award":["UID\/EEA\/00066\/203"],"award-info":[{"award-number":["UID\/EEA\/00066\/203"]}]},{"DOI":"10.13039\/100001245","name":"JMF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001245","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Each cell is a phenotypically unique individual that is influenced by internal and external processes, operating in parallel. To characterize the dynamics of cellular processes one needs to observe many individual cells from multiple points of view and over time, so as to identify commonalities and variability. With this aim, we engineered a software, \u2018SCIP\u2019, to analyze multi-modal, multi-process, time-lapse microscopy morphological and functional images. SCIP is capable of automatic and\/or manually corrected segmentation of cells and lineages, automatic alignment of different microscopy channels, as well as detect, count and characterize fluorescent spots (such as RNA tagged by MS2-GFP), nucleoids, Z rings, Min system, inclusion bodies, undefined structures, etc. The results can be exported into *mat files and all results can be jointly analyzed, to allow studying not only each feature and process individually, but also find potential relationships. While we exemplify its use on Escherichia coli, many of its functionalities are expected to be of use in analyzing other prokaryotes and eukaryotic cells as well. We expect SCIP to facilitate the finding of relationships between cellular processes, from small-scale (e.g. gene expression) to large-scale (e.g. cell division), in single cells and cell lineages.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/www.ca3-uninova.org\/project_scip<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty505","type":"journal-article","created":{"date-parts":[[2018,6,19]],"date-time":"2018-06-19T19:24:19Z","timestamp":1529436259000},"page":"4318-4320","source":"Crossref","is-referenced-by-count":5,"title":["SCIP: a single-cell image processor toolbox"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3351-2910","authenticated-orcid":false,"given":"Leonardo","family":"Martins","sequence":"first","affiliation":[{"name":"Faculty of Biomedical Sciences and Engineering and Laboratory of Biosystem Dynamics of the BioMediTech Institute, Tampere University of Technology, Tampere, Finland"},{"name":"Faculty of Sciences and Technology, Department of Electrical Engineering and CA3 Group of UNINOVA\/CTS, NOVA University of Lisbon, Caparica, Portugal"}]},{"given":"Ramakanth","family":"Neeli-Venkata","sequence":"additional","affiliation":[{"name":"Faculty of Biomedical Sciences and Engineering and Laboratory of Biosystem Dynamics of the BioMediTech Institute, Tampere University of Technology, Tampere, Finland"}]},{"given":"Samuel M D","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Faculty of Biomedical Sciences and Engineering and Laboratory of Biosystem Dynamics of the BioMediTech Institute, Tampere University of Technology, Tampere, Finland"}]},{"given":"Antti","family":"H\u00e4kkinen","sequence":"additional","affiliation":[{"name":"Faculty of Biomedical Sciences and Engineering and Laboratory of Biosystem Dynamics of the BioMediTech Institute, Tampere University of Technology, Tampere, Finland"}]},{"given":"Andre S","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"Faculty of Biomedical Sciences and Engineering and Laboratory of Biosystem Dynamics of the BioMediTech Institute, Tampere University of Technology, Tampere, Finland"},{"name":"Faculty of Sciences and Technology, Department of Electrical Engineering and CA3 Group of UNINOVA\/CTS, NOVA University of Lisbon, Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7173-7374","authenticated-orcid":false,"given":"Jos\u00e9 M","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Faculty of Sciences and Technology, Department of Electrical Engineering and CA3 Group of UNINOVA\/CTS, NOVA University of Lisbon, Caparica, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2018,6,21]]},"reference":[{"key":"2023012712254270500_bty505-B1","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1016\/j.cell.2011.11.001","article-title":"Computer vision in cell biology","volume":"147","author":"Danuser","year":"2011","journal-title":"Cell"},{"key":"2023012712254270500_bty505-B2","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1093\/bioinformatics\/btt194","article-title":"CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli","volume":"29","author":"H\u00e4kkinen","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712254270500_bty505-B3","doi-asserted-by":"crossref","first-page":"71","DOI":"10.2144\/000112257","article-title":"CellProfilerTM: free, versatile software for automated biological image analysis","volume":"42","author":"Lamprecht","year":"2007","journal-title":"Biotechniques"},{"key":"2023012712254270500_bty505-B4","doi-asserted-by":"crossref","first-page":"2512","DOI":"10.1016\/j.bpj.2016.10.024","article-title":"Polar localization of the serine chemoreceptor of Escherichia coli is nucleoid exclusion-dependent","volume":"111","author":"Neeli-Venkata","year":"2016","journal-title":"Biophys. 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