{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T06:37:45Z","timestamp":1725863865540},"publisher-location":"Cham","reference-count":26,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319458854"},{"type":"electronic","value":"9783319458861"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-3-319-45886-1_9","type":"book-chapter","created":{"date-parts":[[2016,8,26]],"date-time":"2016-08-26T08:41:50Z","timestamp":1472200910000},"page":"105-116","source":"Crossref","is-referenced-by-count":3,"title":["Automated Segmentation of Immunostained Cell Nuclei in 3D Ultramicroscopy Images"],"prefix":"10.1007","author":[{"given":"Aaron","family":"Scherzinger","sequence":"first","affiliation":[]},{"given":"Florian","family":"Kleene","sequence":"additional","affiliation":[]},{"given":"Cathrin","family":"Dierkes","sequence":"additional","affiliation":[]},{"given":"Friedemann","family":"Kiefer","sequence":"additional","affiliation":[]},{"given":"Klaus H.","family":"Hinrichs","sequence":"additional","affiliation":[]},{"given":"Xiaoyi","family":"Jiang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,8,27]]},"reference":[{"key":"9_CR1","unstructured":"The FARSight toolkit. http:\/\/www.farsight-toolkit.org"},{"issue":"4","key":"9_CR2","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1109\/TBME.2009.2035102","volume":"57","author":"Y Al-Kofahi","year":"2010","unstructured":"Al-Kofahi, Y., Lassoued, W., Lee, W., Roysam, B.: Improved automatic detection and segmentation of cell nuclei in histopathology images. IEEE Trans. Biomed. Eng. 57(4), 841\u2013852 (2010)","journal-title":"IEEE Trans. Biomed. Eng."},{"key":"9_CR3","doi-asserted-by":"crossref","unstructured":"Bergeest, J.P., Rohr, K.: Segmentation of cell nuclei in 3D microscopy images based on level set deformable models and convex minimization. In: 11th IEEE International Symposium on Biomedical Imaging (ISBI), pp. 637\u2013640 (2014)","DOI":"10.1109\/ISBI.2014.6867951"},{"key":"9_CR4","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1007\/978-3-642-02230-2_42","volume-title":"Image Analysis","author":"O Dan\u011bk","year":"2009","unstructured":"Dan\u011bk, O., Matula, P., Ortiz-de-Sol\u00f3rzano, C., Mu\u00f1oz-Barrutia, A., Ma\u0161ka, M., Kozubek, M.: Segmentation of touching cell nuclei using a two-stage graph cut model. In: Salberg, A.-B., Hardeberg, J.Y., Jenssen, R. (eds.) SCIA 2009. LNCS, vol. 5575, pp. 410\u2013419. Springer, Heidelberg (2009)"},{"key":"9_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1007\/11550518_47","volume-title":"Pattern Recognition","author":"J Fehr","year":"2005","unstructured":"Fehr, J., Ronneberger, O., Kurz, H., Burkhardt, H.: Self-learning segmentation and classification of cell-nuclei in 3D volumetric data using voxel-wise gray scale invariants. In: Kropatsch, W.G., Sablatnig, R., Hanbury, A. (eds.) DAGM 2005. LNCS, vol. 3663, pp. 377\u2013384. Springer, Heidelberg (2005)"},{"issue":"1","key":"9_CR6","first-page":"3133","volume":"15","author":"M Fern\u00e1ndez-Delgado","year":"2014","unstructured":"Fern\u00e1ndez-Delgado, M., Cernadas, E., Barro, S., Amorim, D.: Do we need hundreds of classifiers to solve real world classification problems? J. Mach. Learn. Res. 15(1), 3133\u20133181 (2014)","journal-title":"J. Mach. Learn. Res."},{"key":"9_CR7","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.compbiomed.2015.04.025","volume":"69","author":"A Gertych","year":"2016","unstructured":"Gertych, A., Ma, Z., Tajbakhsh, J., Vel\u00e1squez-Vacca, A., Knudsen, B.S.: Rapid 3-D delineation of cell nuclei for high-content screening platforms. Comput. Biol. Med. 69, 328\u2013338 (2016)","journal-title":"Comput. Biol. Med."},{"key":"9_CR8","doi-asserted-by":"crossref","unstructured":"Harder, N., Bodnar, M., Eils, R., Spector, D.L., Rohr, K.: 3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp. 216\u2013219 (2011)","DOI":"10.1109\/ISBI.2011.5872391"},{"issue":"1","key":"9_CR9","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1111\/j.1365-2818.2010.03482.x","volume":"243","author":"C Indhumathi","year":"2011","unstructured":"Indhumathi, C., Cai, Y., Guan, Y., Opas, M.: An automatic segmentation algorithm for 3D cell cluster splitting using volumetric confocal images. J. Microsc. 243(1), 60\u201376 (2011)","journal-title":"J. Microsc."},{"issue":"1","key":"9_CR10","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1002\/cyto.a.10079","volume":"56","author":"G Lin","year":"2003","unstructured":"Lin, G., Adiga, U., Olson, K., Guzowski, J.F., Barnes, C.A., Roysam, B.: A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal image stacks. Cytometry Part A 56(1), 23\u201336 (2003)","journal-title":"Cytometry Part A"},{"issue":"1","key":"9_CR11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-015-0617-x","volume":"16","author":"B Mathew","year":"2015","unstructured":"Mathew, B., Schmitz, A., Mu\u00f1oz-Descalzo, S., Ansari, N., Pampaloni, F., Stelzer, E., Fischer, S.: Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with lines-of-sight decomposition. BMC Bioinform. 16(1), 1\u201314 (2015)","journal-title":"BMC Bioinform."},{"issue":"10","key":"9_CR12","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nmeth.1709","volume":"8","author":"J Mertz","year":"2011","unstructured":"Mertz, J.: Optical sectioning microscopy with planar or structured illumination. Nat. Methods 8(10), 811\u2013819 (2011)","journal-title":"Nat. Methods"},{"issue":"6","key":"9_CR13","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1109\/MCG.2009.130","volume":"29","author":"J Meyer-Spradow","year":"2009","unstructured":"Meyer-Spradow, J., Ropinski, T., Mensmann, J., Hinrichs, K.H.: Voreen: a rapid-prototyping environment for ray-casting-based volume visualizations. IEEE Comput. Graphics Appl. (Appl. Dept.) 29(6), 6\u201313 (2009)","journal-title":"IEEE Comput. Graphics Appl. (Appl. Dept.)"},{"issue":"14","key":"9_CR14","doi-asserted-by":"crossref","first-page":"1840","DOI":"10.1093\/bioinformatics\/btt276","volume":"29","author":"J Ollion","year":"2013","unstructured":"Ollion, J., Cochennec, J., Loll, F., Escud\u00e9, C., Boudier, T.: TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. Bioinformatics 29(14), 1840\u20131841 (2013)","journal-title":"Bioinformatics"},{"issue":"3","key":"9_CR15","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1016\/j.patcog.2006.06.025","volume":"40","author":"V Osma-Ruiz","year":"2007","unstructured":"Osma-Ruiz, V., Godino-Llorente, J.I., S\u00e1enz-Lech\u00f3n, N., G\u00f3mez-Vilda, P.: An improved watershed algorithm based on efficient computation of shortest paths. Pattern Recogn. 40(3), 1078\u20131090 (2007)","journal-title":"Pattern Recogn."},{"issue":"1","key":"9_CR16","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1111\/jmi.12096","volume":"253","author":"J Qi","year":"2014","unstructured":"Qi, J.: Dense nuclei segmentation based on graph cut and convexity-concavity analysis. J. Microsc. 253(1), 42\u201353 (2014)","journal-title":"J. Microsc."},{"issue":"1","key":"9_CR17","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/nmeth.3222","volume":"12","author":"EG Reynaud","year":"2015","unstructured":"Reynaud, E.G., Peychl, J., Huisken, J., Tomancak, P.: Guide to light-sheet microscopy for adventurous biologists. Nat. Methods 12(1), 30\u201334 (2015)","journal-title":"Nat. Methods"},{"issue":"7","key":"9_CR18","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J.Y., White, D.J., Hartenstein, V., Eliceiri, K., Tomancak, P., Cardona, A.: Fiji: an open-source platform for biological-image analysis. Nat. Methods 9(7), 676\u2013682 (2012)","journal-title":"Nat. Methods"},{"issue":"1","key":"9_CR19","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1117\/1.1631315","volume":"13","author":"M Sezgin","year":"2004","unstructured":"Sezgin, M., Sankur, B.: Survey over image thresholding techniques and quantitative performance evaluation. J. Electron. Imaging 13(1), 146\u2013168 (2004)","journal-title":"J. Electron. Imaging"},{"key":"9_CR20","volume-title":"Morphological Image Analysis: Principles and Applications","author":"P Soille","year":"2003","unstructured":"Soille, P.: Morphological Image Analysis: Principles and Applications, 2nd edn. Springer, Heidelberg (2003)","edition":"2"},{"key":"9_CR21","doi-asserted-by":"crossref","unstructured":"Sommer, C., Straehle, C.N., K\u00f6the, U., Hamprecht, F.A.: Ilastik: interactive learning and segmentation toolkit. In: 8th IEEE International Symposium on Biomedical Imaging (ISBI), pp. 230\u2013233. IEEE (2011)","DOI":"10.1109\/ISBI.2011.5872394"},{"issue":"1","key":"9_CR22","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/nmeth.3219","volume":"12","author":"EHK Stelzer","year":"2015","unstructured":"Stelzer, E.H.K.: Light-sheet fluorescence microscopy for quantitative biology. Nat. Methods 12(1), 23\u201326 (2015)","journal-title":"Nat. Methods"},{"key":"9_CR23","doi-asserted-by":"crossref","unstructured":"Tek, F.B., Kroeger, T., Mikula, S., Hamprecht, F.A.: Automated cell nucleus detection for large-volume electron microscopy of neural tissue. In: 11th IEEE International Symposium on Biomedical Imaging (ISBI), pp. 69\u201372 (2014)","DOI":"10.1109\/ISBI.2014.6867811"},{"issue":"1","key":"9_CR24","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1111\/j.0022-2720.2004.01338.x","volume":"215","author":"C W\u00e4hlby","year":"2004","unstructured":"W\u00e4hlby, C., Sintorn, I.M., Erlandsson, F., Borgefors, G., Bengtsson, E.: Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections. J. Microsc. 215(1), 67\u201376 (2004)","journal-title":"J. Microsc."},{"key":"9_CR25","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/srep00503","volume":"2","author":"S Wienert","year":"2012","unstructured":"Wienert, S., Heim, D., Saeger, K., Stenzinger, A., Beil, M., Hufnagl, P., Dietel, M., Denkert, C., Klauschen, F.: Dense nuclei segmentation based on graph cut and convexity-concavity analysis. Sci. Rep. 2, 503\u2013510 (2012)","journal-title":"Sci. Rep."},{"issue":"3","key":"9_CR26","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1038\/nprot.2011.441","volume":"7","author":"T Yokomizo","year":"2012","unstructured":"Yokomizo, T., Yamada-Inagawa, T., Yzaguirre, A.D., Chen, M.J., Speck, N.A., Dzierzak, E.: Whole-mount three-dimensional imaging of internally localized immunostained cells within mouse embryos. Nat. Protoc. 7(3), 421\u2013431 (2012)","journal-title":"Nat. Protoc."}],"container-title":["Lecture Notes in Computer Science","Pattern Recognition"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-45886-1_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T17:27:34Z","timestamp":1498325254000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-45886-1_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319458854","9783319458861"],"references-count":26,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-45886-1_9","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2016]]}}}