{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T06:36:36Z","timestamp":1787726196490,"version":"build-2784847793"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T00:00:00Z","timestamp":1567382400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T00:00:00Z","timestamp":1567382400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-3055-3","type":"journal-article","created":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T14:07:41Z","timestamp":1567433261000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":57,"title":["Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4254-4255","authenticated-orcid":false,"given":"Eric","family":"Czech","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bulent Arman","family":"Aksoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pinar","family":"Aksoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff","family":"Hammerbacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,9,2]]},"reference":[{"key":"3055_CR1","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1016\/j.cell.2016.04.019","volume":"165","author":"MH Spitzer","year":"2016","unstructured":"Spitzer MH, Nolan GP. Mass cytometry: single cells. Cell. 2016;165:780\u201391.","journal-title":"Cell"},{"key":"3055_CR2","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1002\/cyto.a.22888","volume":"89","author":"K Feher","year":"2016","unstructured":"Feher K, von Volkmann K, Kirsch J, Radbruch A, Popien J, Kaiser T. Multispectral flow cytometry: The consequences of increased light collection. Cytometry A. 2016;89:681\u20139.","journal-title":"Cytometry A"},{"key":"3055_CR3","doi-asserted-by":"publisher","first-page":"15580","DOI":"10.1038\/s41598-017-15798-4","volume":"7","author":"S Blom","year":"2017","unstructured":"Blom S, Paavolainen L, Bychkov D, Turkki R, M\u00e4ki-Teeri P, Hemmes A, et al. Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis. Sci Rep. 2017;7:15580.","journal-title":"Sci Rep"},{"key":"3055_CR4","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1038\/nm.3488","volume":"20","author":"M Angelo","year":"2014","unstructured":"Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, et al. Multiplexed ion beam imaging of human breast tumors. Nat Med. 2014;20:436\u201342.","journal-title":"Nat Med"},{"key":"3055_CR5","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1016\/j.cell.2018.07.010","volume":"174","author":"Y Goltsev","year":"2018","unstructured":"Goltsev Y, Samusik N, Kennedy-Darling J, Bhate S, Hale M, Vazquez G, et al. Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging. Cell. 2018;174:968\u201381 e15.","journal-title":"Cell"},{"key":"3055_CR6","doi-asserted-by":"publisher","first-page":"6131","DOI":"10.1021\/acs.nanolett.7b02716","volume":"17","author":"Y Wang","year":"2017","unstructured":"Wang Y, Woehrstein JB, Donoghue N, Dai M, Avenda\u00f1o MS, Schackmann RCJ, et al. Rapid sequential in situ multiplexing with DNA exchange imaging in neuronal cells and tissues. Nano Lett. 2017;17:6131\u20139.","journal-title":"Nano Lett"},{"key":"3055_CR7","doi-asserted-by":"publisher","unstructured":"Lin J-R, Izar B, Wang S, Yapp C, Mei S, Shah PM, et al. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. Elife. 2018;7. \n                    https:\/\/doi.org\/10.7554\/eLife.31657\n                    \n                  .","DOI":"10.7554\/eLife.31657"},{"key":"3055_CR8","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1111\/ijlh.12068","volume":"35","author":"BD Hedley","year":"2013","unstructured":"Hedley BD, Keeney M. Technical issues: flow cytometry and rare event analysis. Int J Lab Hematol. 2013;35:344\u201350.","journal-title":"Int J Lab Hematol"},{"issue":"9","key":"3055_CR9","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1038\/nmeth.4391","volume":"14","author":"Denis Schapiro","year":"2017","unstructured":"Schapiro D, Jackson HW, Raghuraman S, Fischer JR, Zanotelli VRT, Schulz D, et al. Histocat: analysis of cell phenotypes and interactions in multiplex image cytometry data. Nature Methods. 2017:873\u20136. \n                    https:\/\/doi.org\/10.1038\/nmeth.4391\n                    \n                  .","journal-title":"Nature Methods"},{"key":"3055_CR10","volume-title":"KNIME: The Konstanz Information Miner. Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007)","author":"MR Berthold","year":"2007","unstructured":"Berthold MR, Cebron N, Dill F, Gabriel TR, K\u00f6tter T, Meinl T, et al. KNIME: The Konstanz Information Miner. Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007). New York: Springer; 2007."},{"key":"3055_CR11","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1186\/s12859-017-1934-z","volume":"18","author":"CT Rueden","year":"2017","unstructured":"Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, et al. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics. 2017;18:529.","journal-title":"BMC Bioinformatics."},{"key":"3055_CR12","doi-asserted-by":"publisher","unstructured":"Sommer C, Straehle C, Kothe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit: 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. New York: IEEE; 2011. \n                    https:\/\/doi.org\/10.1109\/isbi.2011.5872394\n                    \n                  .","DOI":"10.1109\/isbi.2011.5872394"},{"key":"3055_CR13","doi-asserted-by":"publisher","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","volume":"7","author":"AE Carpenter","year":"2006","unstructured":"Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7:R100.","journal-title":"Genome Biol"},{"key":"3055_CR14","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1186\/1471-2105-9-482","volume":"9","author":"TR Jones","year":"2008","unstructured":"Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, et al. CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics. 2008;9:482.","journal-title":"BMC Bioinformatics."},{"key":"3055_CR15","volume-title":"TensorFlow: Large-scale machine learning on heterogeneous systems","author":"M Abadi","year":"2015","unstructured":"Mart\u00edn Abadi, Ashish Agarwal, Paul Barham, Eugene Brevdo, Zhifeng Chen, Craig Citro, Greg S. Corrado, Andy Davis, Jeffrey Dean, Matthieu Devin, Sanjay Ghemawat, Ian Goodfellow, Andrew Harp, Geoffrey Irving, Michael Isard, Rafal Jozefowicz, Yangqing Jia, Lukasz Kaiser, Manjunath Kudlur, Josh Levenberg, Dan Man\u00e9, Mike Schuster, Rajat Monga, Sherry Moore, Derek Murray, Chris Olah, Jonathon Shlens, Benoit Steiner, Ilya Sutskever, Kunal Talwar, Paul Tucker, Vincent Vanhoucke, Vijay Vasudevan, Fernanda Vi\u00e9gas, Oriol Vinyals, Pete Warden, Martin Wattenberg, Martin Wicke, Yuan Yu, and Xiaoqiang Zheng. TensorFlow: Large-scale machine learning on heterogeneous systems. 2015. Available: \n                    https:\/\/www.tensorflow.org\/"},{"key":"3055_CR16","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1364\/OL.33.000156","volume":"33","author":"M Guizar-Sicairos","year":"2008","unstructured":"Guizar-Sicairos M, Thurman ST, Fienup JR. Efficient subpixel image registration algorithms. Opt Lett. 2008;33:156\u20138.","journal-title":"Opt Lett"},{"key":"3055_CR17","doi-asserted-by":"publisher","first-page":"e453","DOI":"10.7717\/peerj.453","volume":"2","author":"S van der Walt","year":"2014","unstructured":"van der Walt S, Sch\u00f6nberger JL, Nunez-Iglesias J, Boulogne F, Warner JD, Yager N, et al. Scikit-image: image processing in Python. Peer J. 2014;2:e453.","journal-title":"Peer J"},{"key":"3055_CR18","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s12859-018-2087-4","volume":"19","author":"SJ Yang","year":"2018","unstructured":"Yang SJ, Berndl M, Michael Ando D, Barch M, Narayanaswamy A, Christiansen E, et al. Assessing microscope image focus quality with deep learning. BMC Bioinformatics. 2018;19:77.","journal-title":"BMC Bioinformatics"},{"key":"3055_CR19","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.ymeth.2016.12.015","volume":"115","author":"D Sage","year":"2017","unstructured":"Sage D, Donati L, Soulez F, Fortun D, Schmit G, Seitz A, et al. DeconvolutionLab2: an open-source software for deconvolution microscopy. Methods. 2017;115:28\u201341.","journal-title":"Methods."},{"key":"3055_CR20","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1364\/JOSAA.34.001029","volume":"34","author":"J Li","year":"2017","unstructured":"Li J, Xue F, Blu T. Fast and accurate three-dimensional point spread function computation for fluorescence microscopy. J Opt Soc Am A Opt Image Sci Vis. 2017;34:1029\u201334.","journal-title":"J Opt Soc Am A Opt Image Sci Vis"},{"key":"3055_CR21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2005970","volume":"16","author":"C McQuin","year":"2018","unstructured":"McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, et al. CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 2018;16:e2005970.","journal-title":"PLoS Biol"},{"key":"3055_CR22","first-page":"535","volume-title":"Voronoi-Based Segmentation of Cells on Image Manifolds. Lecture Notes in Computer Science","author":"TR Jones","year":"2005","unstructured":"Jones TR, Carpenter A, Golland P. Voronoi-Based Segmentation of Cells on Image Manifolds. Lecture Notes in Computer Science; 2005. p. 535\u201343."},{"key":"3055_CR23","volume-title":"SciPy: Open source scientific tools for Python","author":"Eric Jones and Travis Oliphant and Pearu Peterson and others","year":"2001","unstructured":"Eric Jones and Travis Oliphant and Pearu Peterson and others. SciPy: Open source scientific tools for Python. 2001. Available: \n                    http:\/\/www.scipy.org\/"},{"key":"3055_CR24","volume-title":"The OpenCV Library. Dr Dobb\u2019s journal of software tools","author":"G Bradski","year":"2000","unstructured":"Bradski G. The OpenCV Library. Dr Dobb\u2019s journal of software tools; 2000."},{"key":"3055_CR25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003806","volume":"10","author":"G Finak","year":"2014","unstructured":"Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, et al. OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput Biol. 2014;10:e1003806.","journal-title":"PLoS Comput Biol"},{"key":"3055_CR26","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1186\/1471-2105-10-145","volume":"10","author":"K Lo","year":"2009","unstructured":"Lo K, Hahne F, Brinkman RR, Gottardo R. Flowclust: a Bioconductor package for automated gating of flow cytometry data. BMC Bioinformatics. 2009;10:145.","journal-title":"BMC Bioinformatics"},{"key":"3055_CR27","doi-asserted-by":"publisher","DOI":"10.7287\/peerj.preprints.26993v1","volume-title":"Human primary T cells: a practical guide","author":"BA Aksoy","year":"2018","unstructured":"Aksoy BA, Aksoy P, Wyatt M, Paulos C, Hammerbacher J. Human primary T cells: a practical guide; 2018. \n                    https:\/\/doi.org\/10.7287\/peerj.preprints.26993v1\n                    \n                  ."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3055-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-3055-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3055-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T19:09:31Z","timestamp":1598900971000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-3055-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,2]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["3055"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-3055-3","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/460980","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,2]]},"assertion":[{"value":"16 January 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 September 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"448"}}