{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T16:24:35Z","timestamp":1773937475273,"version":"3.50.1"},"publisher-location":"Cham","reference-count":37,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783319547169","type":"print"},{"value":"9783319547176","type":"electronic"}],"license":[{"start":{"date-parts":[[2017,1,1]],"date-time":"2017-01-01T00:00:00Z","timestamp":1483228800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017]]},"DOI":"10.1007\/978-3-319-54717-6_3","type":"book-chapter","created":{"date-parts":[[2017,3,2]],"date-time":"2017-03-02T20:53:00Z","timestamp":1488487980000},"page":"41-55","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["SynapCountJ: A Validated Tool for Analyzing Synaptic Densities in Neurons"],"prefix":"10.1007","author":[{"given":"Gadea","family":"Mata","sequence":"first","affiliation":[]},{"given":"Germ\u00e1n","family":"Cuesto","sequence":"additional","affiliation":[]},{"given":"J\u00f3nathan","family":"Heras","sequence":"additional","affiliation":[]},{"given":"Miguel","family":"Morales","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Romero","sequence":"additional","affiliation":[]},{"given":"Julio","family":"Rubio","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,3,4]]},"reference":[{"key":"3_CR1","unstructured":"Formath: formalisation of mathematics (2010\u20132013). \n                    http:\/\/wiki.portal.chalmers.se\/cse\/pmwiki.php\/ForMath\/ForMath"},{"key":"3_CR2","unstructured":"Amorim, A., et al.: A verified information-flow architecture. In: 41st ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages (POPL 2014) (2014)"},{"issue":"4","key":"3_CR3","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1007\/s10817-007-9094-x","volume":"40","author":"J Aransay","year":"2008","unstructured":"Aransay, J., Ballarin, C., Rubio, J.: A mechanized proof of the Basic Perturbation Lemma. J. Autom. Reasoning 40(4), 271\u2013292 (2008)","journal-title":"J. Autom. Reasoning"},{"key":"3_CR4","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0166-218X(02)00221-4","volume":"125","author":"R Ayala","year":"2003","unstructured":"Ayala, R., Dom\u00ednguez, E., Franc\u00e9s, A., Quintero, A.: Homotopy in digital spaces. Discrete Appl. Math. 125, 3\u201324 (2003)","journal-title":"Discrete Appl. Math."},{"key":"3_CR5","unstructured":"Benton, N.: Machine Obstructed Proof: how many months can it take to verify 30 assembly instructions? (2006)"},{"issue":"8","key":"3_CR6","doi-asserted-by":"publisher","first-page":"2721","DOI":"10.1523\/JNEUROSCI.4477-10.2011","volume":"31","author":"G Cuesto","year":"2011","unstructured":"Cuesto, G., Enriquez-Barreto, L., Caram\u00e9s, C., et al.: Phosphoinositide-3-kinase activation controls synaptogenesis and spinogenesis in hippocampal neurons. J. Neurosci. 31(8), 2721\u20132733 (2011)","journal-title":"J. Neurosci."},{"issue":"3","key":"3_CR7","doi-asserted-by":"publisher","first-page":"e0118475","DOI":"10.1371\/journal.pone.0118475","volume":"10","author":"G Cuesto","year":"2015","unstructured":"Cuesto, G., Jord\u00e1n-\u00c1lvarez, S., Enriquez-Barreto, L., et al.: GSK3\n                    \n                      \n                    \n                    $$\\beta $$\n                   inhibition promotes synaptogenesis in Drosophila and mammalian neurons. Plos One 10(3), e0118475 (2015). doi:\n                    10.1371\/journal.pone.0118475","journal-title":"Plos One"},{"issue":"12","key":"3_CR8","doi-asserted-by":"publisher","first-page":"e115298","DOI":"10.1371\/journal.pone.0115298","volume":"9","author":"E Danielson","year":"2014","unstructured":"Danielson, E., Lee, S.H.: SynPAnal: software for rapid quantification of the density and intensity of protein puncta from fluorescence microscopy images of neurons. PLoS ONE 9(12), e115298 (2014). doi:\n                    10.1371\/journal.pone.0115298","journal-title":"PLoS ONE"},{"issue":"5","key":"3_CR9","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1097\/NEN.0b013e318217a118","volume":"70","author":"B DaRocha-Souto","year":"2003","unstructured":"DaRocha-Souto, B., Scotton, T.C., Coma, M., et al.: Brain oligomeric \n                    \n                      \n                    \n                    $$\\beta $$\n                  -amyloid but not total amyloid plaque burden correlates with neuronal loss and astrocyte inflammatory response in amyloid precursor protein\/tau transgenic mice. J. Neuropathol. Exp. Neurol. 70(5), 360\u2013376 (2003)","journal-title":"J. Neuropathol. Exp. Neurol."},{"key":"3_CR10","unstructured":"Devices, M.: Metamorph research imaging (2015). \n                    http:\/\/www.moleculardevices.com\/systems\/metamorph-research-imaging"},{"key":"3_CR11","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1016\/j.tcs.2010.11.016","volume":"412","author":"C Dom\u00ednguez","year":"2011","unstructured":"Dom\u00ednguez, C., Rubio, J.: Effective homology of bicomplexes, formalized in Coq. Theor. Comput. Sci. 412, 962\u2013970 (2011)","journal-title":"Theor. Comput. Sci."},{"key":"3_CR12","unstructured":"Dousson, X., Rubio, J., Sergeraert, F., Siret, Y.: The Kenzo program. Institut Fourier, Grenoble (1998). \n                    https:\/\/www-fourier.ujf-grenoble.fr\/~sergerar\/Kenzo\/"},{"issue":"29","key":"3_CR13","doi-asserted-by":"publisher","first-page":"6573","DOI":"10.1523\/JNEUROSCI.1580-04.2004","volume":"24","author":"B Franco","year":"2004","unstructured":"Franco, B., Bogdanik, L., Bobinnec, Y., et al.: Shaggy, the homolog of glycogen synthase kinase 3, controls neuromuscular junction growth in Drosophila. J. Neurosci. 24(29), 6573\u20136577 (2004)","journal-title":"J. Neurosci."},{"issue":"2\u20133","key":"3_CR14","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.dam.2004.09.014","volume":"147","author":"R Gonz\u00e1lez-D\u00edaz","year":"2005","unstructured":"Gonz\u00e1lez-D\u00edaz, R., Real, P.: On the Cohomology of 3D digital images. Discrete Appl. Math. 147(2\u20133), 245\u2013263 (2005)","journal-title":"Discrete Appl. Math."},{"key":"3_CR15","unstructured":"Hales, T.: The Flyspeck Project fact sheet (2005). Project description available at \n                    http:\/\/code.google.com\/p\/flyspeck\/"},{"key":"3_CR16","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-3-642-27549-4_15","volume-title":"Computer Aided Systems Theory \u2013 EUROCAST 2011","author":"J Heras","year":"2012","unstructured":"Heras, J., Pascual, V., Rubio, J.: A certified module to study digital images with the Kenzo system. In: Moreno-D\u00edaz, R., Pichler, F., Quesada-Arencibia, A. (eds.) EUROCAST 2011. LNCS, vol. 6927, pp. 113\u2013120. Springer, Heidelberg (2012)"},{"key":"3_CR17","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/978-3-642-30238-1_6","volume-title":"Computational Topology in Image Context","author":"J Heras","year":"2012","unstructured":"Heras, J., D\u00e9n\u00e8s, M., Mata, G., M\u00f6rtberg, A., Poza, M., Siles, V.: Towards a certified computation of homology groups for digital images. In: Ferri, M., Frosini, P., Landi, C., Cerri, A., Fabio, B. (eds.) CTIC 2012. LNCS, vol. 7309, pp. 49\u201357. Springer, Heidelberg (2012)"},{"issue":"1","key":"3_CR18","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1093\/jigpal\/jzt034","volume":"22","author":"L Lamb\u00e1n","year":"2013","unstructured":"Lamb\u00e1n, L., Mart\u00edn-Mateos, F.J., Rubio, J., Ruiz-Reina, J.L.: Verifying the bridge between simplicial topology and algebra: the Eilenberg-Zilber algorithm. Logic J. IGpPL 22(1), 39\u201365 (2013)","journal-title":"Logic J. IGpPL"},{"issue":"5","key":"3_CR19","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1083\/jcb.201004104","volume":"189","author":"M Linkert","year":"2010","unstructured":"Linkert, M., Rueden, C.T., Allan, C., et al.: Metadata matters: access to image data in the real world. J. Cell Biol. 189(5), 777\u2013782 (2010)","journal-title":"J. Cell Biol."},{"issue":"1","key":"3_CR20","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.patrec.2015.05.010","volume":"62","author":"G Mata","year":"2015","unstructured":"Mata, G., et al.: Zigzag persistent homology for processing neuronal images. Pattern Recogn. Lett. 62(1), 55\u201360 (2015)","journal-title":"Pattern Recogn. Lett."},{"key":"3_CR21","doi-asserted-by":"crossref","unstructured":"Mata, G., et al.: Automatic detection of neurons in high-content microscope images using machine learning approaches. In: Proceedings of the 13th IEEE International Symposium on Biomedical Imaging (ISBI 2016). IEEE Xplore (2016)","DOI":"10.1109\/ISBI.2016.7493276"},{"issue":"2","key":"3_CR22","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1002\/cyto.a.20022","volume":"58","author":"E Meijering","year":"2004","unstructured":"Meijering, E., Jacob, M., Sarria, J.C.F., et al.: Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry Part A 58(2), 167\u2013176 (2004)","journal-title":"Cytometry Part A"},{"issue":"3","key":"3_CR23","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/S0896-6273(00)00064-7","volume":"27","author":"M Morales","year":"2000","unstructured":"Morales, M., Colicos, M.A., Goda, Y.: Actin-dependent regulation of neurotransmitter release at central synapses. Neuron 27(3), 539\u2013550 (2000)","journal-title":"Neuron"},{"key":"3_CR24","volume-title":"Elements of Algebraic Topology","author":"JR Munkres","year":"1984","unstructured":"Munkres, J.R.: Elements of Algebraic Topology. Addison-Wesley, Reading (1984)"},{"key":"3_CR25","unstructured":"de Gre\u00f1u de Pedro, J.D.: An\u00e1lisis Matem\u00e1tico de rutinas de procesamiento de im\u00e1genes digitales en Fiji\/ImageJ. Technical report, Universidad de La Rioja (2014)"},{"issue":"3","key":"3_CR26","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1145\/2630789","volume":"15","author":"M Poza","year":"2014","unstructured":"Poza, M., Dom\u00ednguez, C., Heras, J., Rubio, J.: A certified reduction strategy for homological image processing. ACM Trans. Comput. Logic 15(3), 23 (2014)","journal-title":"ACM Trans. Comput. Logic"},{"key":"3_CR27","unstructured":"Romero, A., Heras, J., Rubio, J., Sergeraert, F.: Defining and computing persistent Z-homology in the general case. CoRR abs\/1403.7086 (2014)"},{"key":"3_CR28","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1090\/S0025-5718-2013-02680-4","volume":"82","author":"A Romero","year":"2013","unstructured":"Romero, A., Rubio, J.: Homotopy groups of suspended classifying spaces: an experimental approach. Math. Comput. 82, 2237\u20132244 (2013)","journal-title":"Math. Comput."},{"key":"3_CR29","unstructured":"Romero, A., Sergeraert, F.: Discrete Vector Fields and Fundamental Algebraic Topology (2010). \n                    http:\/\/arxiv.org\/abs\/1005.5685v1"},{"issue":"7","key":"3_CR30","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J., Argand-Carreras, I., Frise, E., et al.: Fiji: an open-source platform for biological-image analysis. Nat. Methods 9(7), 676\u2013682 (2012)","journal-title":"Nat. Methods"},{"issue":"2","key":"3_CR31","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.jneumeth.2010.12.011","volume":"195","author":"SK Schmitz","year":"2011","unstructured":"Schmitz, S.K., Hjorth, J.J.J., Joemail, R.M.S., et al.: Automated analysis of neuronal morphology, synapse number and synaptic recruitment. J. Neurosci. Methods 195(2), 185\u2013193 (2011)","journal-title":"J. Neurosci. Methods"},{"key":"3_CR32","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nmeth.2089","volume":"9","author":"C Schneider","year":"2012","unstructured":"Schneider, C., Rasband, W., Eliceiri, K.: NIH Image to ImageJ. Nat. Methods 9, 671\u2013675 (2012)","journal-title":"Nat. Methods"},{"key":"3_CR33","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1007\/978-3-540-39903-2_85","volume-title":"Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003","author":"F S\u00e9gonne","year":"2003","unstructured":"S\u00e9gonne, F., Grimson, E., Fischl, B.: Topological correction of subcortical segmentation. In: Ellis, R.E., Peters, T.M. (eds.) MICCAI 2003. LNCS, vol. 2879, pp. 695\u2013702. Springer, Heidelberg (2003)"},{"issue":"5594","key":"3_CR34","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1126\/science.1074069","volume":"298","author":"DJ Selkoe","year":"2002","unstructured":"Selkoe, D.J.: Alzheimer\u2019s diseases is a synaptic failure. Science 298(5594), 789\u2013791 (2002)","journal-title":"Science"},{"key":"3_CR35","unstructured":"Sergeraert, F.: Effective homology, a survey. Technical report, Institut Fourier (1992). \n                    http:\/\/www-fourier.ujf-grenoble.fr\/sergerar\/Papers\/Survey.pdf"},{"key":"3_CR36","unstructured":"Shiwarski, D.J., Dagda, R.D., Chu, C.T.: Green and red puncta colocalization (2014). \n                    http:\/\/imagejdocu.tudor.lu\/doku.php?id=plugin:analysis:colocalization_analysis_macro_for_red_and_green_puncta:start"},{"key":"3_CR37","unstructured":"Wark, B.: Puncta analyzer v2.0 (2013). \n                    https:\/\/github.com\/physion\/puncta-analyzer"}],"container-title":["Communications in Computer and Information Science","Biomedical Engineering Systems and Technologies"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-54717-6_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T23:16:02Z","timestamp":1558394162000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-54717-6_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"ISBN":["9783319547169","9783319547176"],"references-count":37,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-54717-6_3","relation":{},"ISSN":["1865-0929","1865-0937"],"issn-type":[{"value":"1865-0929","type":"print"},{"value":"1865-0937","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017]]},"assertion":[{"value":"4 March 2017","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"BIOSTEC","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Joint Conference on Biomedical Engineering Systems and Technologies","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Rome","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Italy","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2016","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"21 February 2016","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"23 February 2016","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"9","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"biostec2016","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/biostec.org\/?y=2016","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}