{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T17:38:43Z","timestamp":1770917923412,"version":"3.50.1"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,5,26]],"date-time":"2017-05-26T00:00:00Z","timestamp":1495756800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,5,26]],"date-time":"2017-05-26T00:00:00Z","timestamp":1495756800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01-GM098151-01"],"award-info":[{"award-number":["R01-GM098151-01"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P41 GM103545-18"],"award-info":[{"award-number":["P41 GM103545-18"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI-1339881"],"award-info":[{"award-number":["ACI-1339881"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS-1162013"],"award-info":[{"award-number":["IIS-1162013"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1694-9","type":"journal-article","created":{"date-parts":[[2017,5,26]],"date-time":"2017-05-26T13:51:22Z","timestamp":1495806682000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2519-0758","authenticated-orcid":false,"given":"Yong","family":"Wan","sequence":"first","affiliation":[]},{"given":"Hideo","family":"Otsuna","sequence":"additional","affiliation":[]},{"given":"Holly A.","family":"Holman","sequence":"additional","affiliation":[]},{"given":"Brig","family":"Bagley","sequence":"additional","affiliation":[]},{"given":"Masayoshi","family":"Ito","sequence":"additional","affiliation":[]},{"given":"A. Kelsey","family":"Lewis","sequence":"additional","affiliation":[]},{"given":"Mary","family":"Colasanto","sequence":"additional","affiliation":[]},{"given":"Gabrielle","family":"Kardon","sequence":"additional","affiliation":[]},{"given":"Kei","family":"Ito","sequence":"additional","affiliation":[]},{"given":"Charles","family":"Hansen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,5,26]]},"reference":[{"key":"1694_CR1","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1016\/j.cell.2007.01.040","volume":"128","author":"GS Jefferis","year":"2007","unstructured":"Jefferis GS, Potter CJ, Chan AM, Marin EC, Rohlfing T, Maurer CR, et al. Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation. Cell. 2007;128:1187\u2013203.","journal-title":"Cell."},{"key":"1694_CR2","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nmeth.1602","volume":"8","author":"H Peng","year":"2011","unstructured":"Peng H, Chung P, Long F, Qu L, Jenett A, Seeds AM, et al. BrainAligner: 3D registration atlases of Drosophila brains. Nat Methods. 2011;8:493\u20138.","journal-title":"Nat Methods"},{"key":"1694_CR3","doi-asserted-by":"publisher","first-page":"1489","DOI":"10.1109\/TVCG.2009.118","volume":"15","author":"Y Wan","year":"2009","unstructured":"Wan Y, Otsuna H, Chien C, Hansen C. An interactive visualization tool for multi-channel confocal microscopy data in neurobiology research. IEEE Trans Vis Comput Graph. 2009;15:1489\u201396.","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"1694_CR4","doi-asserted-by":"crossref","unstructured":"Wan Y, Otsuna H, Chien C, Hansen C. Interactive extraction of neural structures with user-guided morphological diffusion. Proceedings of the IEEE BioVis. IEEE;2012. p. 1-8.","DOI":"10.1109\/BioVis.2012.6378577"},{"key":"1694_CR5","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1016\/j.cub.2013.03.015","volume":"23","author":"M Ito","year":"2013","unstructured":"Ito M, Masuda N, Shinomiya K, Endo K, Ito K. Systematic analysis of neural projections reveals clonal composition of the Drosophila brain. Curr Biol. 2013;23:644\u201355.","journal-title":"Curr Biol."},{"key":"1694_CR6","volume":"3","author":"Y Aso","year":"2014","unstructured":"Aso Y, Hattori D, Yu Y, Johnston RM, Iyer NA, Ngo T, et al. The neuronal architecture of the mushroom body provides a logic for associative learning. eLife. 2014;3, e04577.","journal-title":"eLife."},{"key":"1694_CR7","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1002\/cne.23705","volume":"523","author":"T Wolff","year":"2015","unstructured":"Wolff T, Iyer NA, Rubin GM. Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits. J Comp Neurol. 2015;523:997\u20131037.","journal-title":"J Comp Neurol."},{"key":"1694_CR8","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1242\/dmm.025874","volume":"9","author":"MP Colasanto","year":"2016","unstructured":"Colasanto MP, Eyal S, Mohassel P, Bamshad M, Bonnemann CG, Zelzer E, et al. Development of a subset of forelimb muscles and their attachment sites requires the ulnar-mammary syndrome gene Tbx3. Dis Model Mech. 2016;9:1257\u201369.","journal-title":"Dis Model Mech."},{"key":"1694_CR9","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1038\/nprot.2014.011","volume":"9","author":"H Peng","year":"2014","unstructured":"Peng H, Bria A, Zhou Z, Iannello G, Long F. Extensible visualization and analysis for multidimensional images using Vaa3D. Nat Protoc. 2014;9:193\u2013208.","journal-title":"Nat Protoc."},{"key":"1694_CR10","doi-asserted-by":"publisher","first-page":"2285","DOI":"10.1109\/TVCG.2012.240","volume":"18","author":"H Hadwiger","year":"2012","unstructured":"Hadwiger H, Beyer J, Jeong W, Pfister H. Interactive volume exploration of petascale microscopy data streams using a visualization-driven virtual memory approach. IEEE Trans Vis Comput Graph. 2012;18:2285\u201394.","journal-title":"IEEE Trans Vis Comput Graph."},{"key":"1694_CR11","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1038\/nmeth.3767","volume":"13","author":"A Bria","year":"2016","unstructured":"Bria A, Iannello G, Onofri L, Peng H. TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images. Nat Methods. 2016;13:192\u20134.","journal-title":"Nat Methods."},{"key":"1694_CR12","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1212\/WNL.28.6.517","volume":"28","author":"WH Oldendorf","year":"1978","unstructured":"Oldendorf WH. The quest for an image of brain: a brief historical and technical review of brain imaging techniques. Neurology. 1978;28:517\u201333.","journal-title":"Neurology."},{"key":"1694_CR13","doi-asserted-by":"publisher","first-page":"25","DOI":"10.2144\/000112517","volume":"43","author":"TJ Collins","year":"2007","unstructured":"Collins TJ. ImageJ for microscopy. Biotechniques. 2007;43:25\u201330.","journal-title":"Biotechniques."},{"key":"1694_CR14","doi-asserted-by":"publisher","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, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676\u201382.","journal-title":"Nat Methods."},{"key":"1694_CR15","unstructured":"VTK - The Visualization Toolkit. Kitware, Inc. www.vtk.org (2016). Accessed 9 Nov 2016."},{"key":"1694_CR16","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/s10278-004-1014-6","volume":"17","author":"A Rosset","year":"2004","unstructured":"Rosset A, Spadola L, Ratib O. OsiriX: an open-source software for navigating in multidimensional DICOM images. J Digit Imaging. 2004;17:205\u201316.","journal-title":"J Digit Imaging."},{"key":"1694_CR17","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1016\/j.mri.2012.05.001","volume":"30","author":"A Fedorova","year":"2012","unstructured":"Fedorova A, Beichelb R, Kalpathy-Cramerc J, Finetd J, Fillion-Robind J, Pujola S, et al. 3D Slicer as an image computing platform for the quantitative imaging network. Magn Reson Imaging. 2012;30:1323\u201341.","journal-title":"Magn Reson Imaging."},{"key":"1694_CR18","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/nmeth.2075","volume":"9","author":"FD Chaumont","year":"2012","unstructured":"Chaumont FD, Dallongeville S, Chenouard N, Herv\u00e9 N, Pop S, Provoost T, et al. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods. 2012;9:690\u20136.","journal-title":"Nat Methods."},{"key":"1694_CR19","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1038\/nmeth.2047","volume":"9","author":"P Kankaanp\u00e4\u00e4","year":"2012","unstructured":"Kankaanp\u00e4\u00e4 P, Paavolainen L, Tiitta S, Karjalainen M, P\u00e4iv\u00e4rinne J, Nieminen J, et al. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat Methods. 2012;9:683\u20139.","journal-title":"Nat Methods."},{"key":"1694_CR20","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1038\/nmeth.2084","volume":"9","author":"KW Eliceiri","year":"2012","unstructured":"Eliceiri KW, Berthold MR, Goldberg IG, Ib\u00e1\u00f1ez L, Manjunath BS, Martone ME, et al. Biological imaging software tools. Nat Methods. 2012;9:697\u2013710.","journal-title":"Nat Methods."},{"key":"1694_CR21","unstructured":"Amira 3D Software for Life Sciences | FEI. FEI Company. https:\/\/www.fei.com\/software\/amira-3d-for-life-sciences (2016). Accessed 9 Nov 2016."},{"key":"1694_CR22","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1038\/nbt.1612","volume":"28","author":"H Peng","year":"2010","unstructured":"Peng H, Ruan Z, Long F, Simpson JH, Myers EW. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol. 2010;28:348\u201353.","journal-title":"Nat Biotechnol."},{"key":"1694_CR23","unstructured":"Imaris | 3D and 4D Real-Time Interactive Data Visualization | Bitplane. Bitplane. www.bitplane.com\/imaris\/imaris (2016). Accessed 9 Nov 2016."},{"key":"1694_CR24","unstructured":"Segal M, Akeley K. The OpenGL Graphics System: A Specification. The Khronos Group Inc. 2016. https:\/\/www.opengl.org\/registry\/doc\/glspec45.core.pdf . Accessed 18 Nov 2016."},{"key":"1694_CR25","unstructured":"Howes L. The OpenCL Specification. Khronos OpenCL Working Group. 2015. https:\/\/www.khronos.org\/registry\/cl\/specs\/opencl-2.1.pdf . Accessed 18 Nov 2016."},{"key":"1694_CR26","doi-asserted-by":"crossref","unstructured":"Engel K, Hadwiger M, Kniss JM, Rezk-Salama C, Weiskopf D. Real-Time Volume Graphics. Wellesly: 1st ed. A K Peters, Ltd.; 2006.","DOI":"10.1201\/b10629"},{"key":"1694_CR27","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1109\/38.511","volume":"8","author":"M Levoy","year":"1988","unstructured":"Levoy M. Display of surfaces from volume data. IEEE Comput Graph. 1988;8:29\u201337.","journal-title":"IEEE Comput Graph."},{"key":"1694_CR28","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1109\/42.41482","volume":"8","author":"J Wallis","year":"1989","unstructured":"Wallis J, Miller T, Lerner C, Kleerup E. Three-dimensional display in nuclear medicine. IEEE Trans Med Imag. 1989;8:297\u2013303.","journal-title":"IEEE Trans Med Imag."},{"key":"1694_CR29","doi-asserted-by":"crossref","unstructured":"Wan Y, Otsuna H, Chien C, Hansen C. FluoRender: an application of 2D image space methods for 3D and 4D confocal microscopy data visualization in neurobiology research. Proceedings of the IEEE Pacific Visualization Symposium. IEEE; 2012. p. 201-8.","DOI":"10.1109\/PacificVis.2012.6183592"},{"key":"1694_CR30","unstructured":"IEEE Standard for Floating-Point Arithmetic. IEEE Computer Society. 2008. http:\/\/ieeexplore.ieee.org\/document\/4610935\/ . Accessed 18 Nov 2016."},{"key":"1694_CR31","unstructured":"AMD's 10-bit Video Output Technology. AMD Inc. 2008. https:\/\/www.amd.com\/Documents\/10-Bit.pdf . Accessed 17 Nov 2016."},{"key":"1694_CR32","unstructured":"10 and 12-Bit Grayscale Technology. Nvidia Inc. 2013. http:\/\/www.nvidia.com\/content\/quadro_fx_product_literature\/TB-04631-001_v05.pdf . Accessed 17 Nov 2016."},{"key":"1694_CR33","unstructured":"Reinhard E, Heidrich W, Debevec P, Pattanaik S, Ward G, Myszkowski K. High Dynamic Range Imaging - Acquisition, Display, and Image-Based Lighting. 2nd ed. Burlington: Morgan Kaufmann Publishers Inc.; 2010."},{"key":"1694_CR34","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1111\/j.1467-8659.2007.01012.x","volume":"26","author":"JD Owens","year":"2007","unstructured":"Owens JD, Luebke D, Govindaraju N, Harris M, Kr\u00fcger J, Lefohn A, et al. A survey of general-purpose computation on graphics hardware. Comput Graph Forum. 2007;26:80\u2013113.","journal-title":"Comput Graph Forum."},{"key":"1694_CR35","unstructured":"Wan Y, Otsuna H, Kwan K, Hansen C. Real-time dense nucleus selection from confocal data. Proceedings of Visual Computing for Biology and Medicine. Eurographics; 2014. p. 59-68."},{"key":"1694_CR36","unstructured":"Gonzalez RC, Woods RE. Digital Image Processing. 3rd ed. Upper Saddle River: Prentice Hall; 2007."},{"key":"1694_CR37","doi-asserted-by":"publisher","first-page":"11691","DOI":"10.1523\/JNEUROSCI.1939-14.2014","volume":"34","author":"A P\u00e9zier","year":"2014","unstructured":"P\u00e9zier A, Jezzini SH, Marie B, Blagbum JM. Engrailed alters the specificity of synaptic connections of Drosophila auditory neurons with the giant fiber. J Neuosci. 2014;34:11691\u2013704.","journal-title":"J Neuosci."},{"key":"1694_CR38","doi-asserted-by":"publisher","first-page":"7538","DOI":"10.1523\/JNEUROSCI.0186-10.2010","volume":"30","author":"A Cardona","year":"2010","unstructured":"Cardona A, Saalfeld S, Arganda I, Pereanu W, Schindelin J, Hartenstein V. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. J Neurosci. 2010;30:7538\u201353.","journal-title":"J Neurosci."},{"key":"1694_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cub.2010.11.056","volume":"21","author":"A Chiang","year":"2011","unstructured":"Chiang A, Lin C, Chuang C, Chang H, Hsieh C, Yeh C, et al. Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr Biol. 2011;21:1\u201311.","journal-title":"Curr Biol."},{"key":"1694_CR40","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1038\/nmeth.2076","volume":"9","author":"O Ronneberger","year":"2012","unstructured":"Ronneberger O, Liu K, Rath M, Rue\u00df D, Mueller T, Skibbe H, et al. ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains. Nat Methods. 2012;9:735\u201342.","journal-title":"Nat Methods."},{"key":"1694_CR41","unstructured":"Hennessy JL, Patterson DA. Computer Architecture: A Quantitative Approach. 5th ed. Waltham: Morgan Kaufmann Publishers Inc.; 2011."},{"key":"1694_CR42","unstructured":"Photoshop Inspiration, Photoshop Information | Photoshop.com. Adobe Inc. www.photoshop.com\/ (2016). Accessed 9 Nov 2016."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1694-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-017-1694-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1694-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T20:29:10Z","timestamp":1750278550000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1694-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,26]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1694"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1694-9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,5,26]]},"assertion":[{"value":"29 November 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 May 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 May 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"280"}}