{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T00:05:54Z","timestamp":1770509154054,"version":"3.49.0"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,7,8]],"date-time":"2008-07-08T00:00:00Z","timestamp":1215475200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Source Code Biol Med"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1751-0473-3-13","type":"journal-article","created":{"date-parts":[[2008,7,8]],"date-time":"2008-07-08T15:39:13Z","timestamp":1215531553000},"source":"Crossref","is-referenced-by-count":178,"title":["Wndchrm \u2013 an open source utility for biological image analysis"],"prefix":"10.1186","volume":"3","author":[{"given":"Lior","family":"Shamir","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikita","family":"Orlov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D Mark","family":"Eckley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomasz","family":"Macura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Josiah","family":"Johnston","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilya G","family":"Goldberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,7,8]]},"reference":[{"key":"30_CR1","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1126\/science.1082602","volume":"300","author":"JR Swedlow","year":"2003","unstructured":"Swedlow JR, Goldberg IG, Brauner E, Sorger PK: Image informatics and quantitative analysis of biological images. Science. 2003, 300: 100-102.","journal-title":"Science"},{"key":"30_CR2","doi-asserted-by":"publisher","first-page":"R47","DOI":"10.1186\/gb-2005-6-5-r47","volume":"6","author":"I Goldberg","year":"2005","unstructured":"Goldberg I, Allan C, Burel JM, Creager D, Falconi A, Hochheiser H, Johnston J, Mellen J, Sorger PK, Swedlow JR: Image informatics and quantitative analysis of biological images. Genome Biology. 2005, 6: R47.","journal-title":"Genome Biology"},{"key":"30_CR3","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1007\/978-3-540-71331-9_3","volume-title":"Imaging Cellular and Molecular Biological Functions","author":"JR Swedlow","year":"2007","unstructured":"Swedlow JR: The Open Microscopy Environment: A collaborative data modeling and software development project for biological image informatics. Imaging Cellular and Molecular Biological Functions. Edited by: Spencer L, Frischknecht F. 2007, Berlin: Springer, 71-92."},{"key":"30_CR4","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, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM: CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology. 2006, 7: R100.","journal-title":"Genome Biology"},{"key":"30_CR5","unstructured":"Orlov N, Shamir L, Macura T, Johnston J, Eckley DM, Goldberg I: WND-CHARM \u2013 Multi purpose classification using compound image transforms. Pattern Recognition Letters."},{"key":"30_CR6","volume-title":"Two-dimensional signal and image processing","author":"JS Lim","year":"1990","unstructured":"Lim JS: Two-dimensional signal and image processing. 1990, New Haven: Prentice Hall"},{"key":"30_CR7","volume-title":"Table of integrals, series and products","author":"I Gradshtein","year":"1994","unstructured":"Gradshtein I, Ryzhik I: Table of integrals, series and products. 1994, Academic Press, 5","edition":"5"},{"key":"30_CR8","first-page":"429","volume":"93","author":"D Gabor","year":"1946","unstructured":"Gabor D: Theory of communication. Journal of IEEE. 1946, 93: 429-457.","journal-title":"Journal of IEEE"},{"key":"30_CR9","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1109\/TIP.2002.804262","volume":"11","author":"C Gregorescu","year":"2002","unstructured":"Gregorescu C, Petkov N, Kruizinga P: Comparison of texture features based on gabor filters. IEEE Trans on Image Processing. 2002, 11: 1160-1167.","journal-title":"IEEE Trans on Image Processing"},{"key":"30_CR10","first-page":"702","volume":"1","author":"E Hadjidementriou","year":"2001","unstructured":"Hadjidementriou E, Grossberg M, Nayar S: Spatial information in multiresolution histograms. IEEE Conference on Computer Vision and Pattern Recognition. 2001, 1: 702.","journal-title":"IEEE Conference on Computer Vision and Pattern Recognition"},{"key":"30_CR11","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1109\/TSMC.1978.4309999","volume":"8","author":"H Tamura","year":"1978","unstructured":"Tamura H, Mori S, Yamavaki T: Textural features corresponding to visual perception. IEEE Trans On Systems, Man and Cybernetics. 1978, 8: 460-472.","journal-title":"IEEE Trans On Systems, Man and Cybernetics"},{"key":"30_CR12","first-page":"75","volume-title":"Picture Processing and Psychopictoris","author":"JM Prewitt","year":"1970","unstructured":"Prewitt JM: Object enhancement and extraction. Picture Processing and Psychopictoris. Edited by: Lipkin BS, Rosenfeld A. 1970, New York: New York: Academic, 75-149."},{"key":"30_CR13","first-page":"119","volume-title":"Proc 2nd IEEE International Symposium on Bioinformatics and Biomedical Engineering","author":"RF Murphy","year":"2001","unstructured":"Murphy RF, Velliste M, Yao J, Porreca G: Searching online journals for fluorescence microscopy images depicting protein subcellular location patterns. Proc 2nd IEEE International Symposium on Bioinformatics and Biomedical Engineering. 2001, 119-128."},{"key":"30_CR14","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1109\/TSMC.1979.4310076","volume":"9","author":"N Otsu","year":"1979","unstructured":"Otsu N: A threshold selection method from gray level histograms. IEEE Trans Systems, Man and Cybernetics. 1979, 9: 62-66.","journal-title":"IEEE Trans Systems, Man and Cybernetics"},{"key":"30_CR15","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1109\/T-C.1971.223289","volume":"20","author":"SB Gray","year":"1971","unstructured":"Gray SB: Local properties of binary Images in two dimensions. IEEE Trans on Computers. 1971, 20: 551-561.","journal-title":"IEEE Trans on Computers"},{"key":"30_CR16","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1364\/JOSA.70.000920","volume":"70","author":"M Teague","year":"1980","unstructured":"Teague M: Image analysis via the general theory of moments. Journal of the Optical Society of America. 1980, 70: 920-930.","journal-title":"Journal of the Optical Society of America"},{"key":"30_CR17","first-page":"269","volume":"6","author":"RM Haralick","year":"1973","unstructured":"Haralick RM, Shanmugam K, Dinstein I: Textural features for image classification. IEEE Trans on Systems, Man, and Cybernetics. 1973, 6: 269-285.","journal-title":"IEEE Trans on Systems, Man, and Cybernetics"},{"key":"30_CR18","first-page":"221","volume-title":"Vision Systems \u2013 Segmentation and Pattern Recognition","author":"N Orlov","year":"2007","unstructured":"Orlov N, Johnston J, Macura T, Shamir L, Goldberg I: Computer vision for microscopy applications. Vision Systems \u2013 Segmentation and Pattern Recognition. Edited by: Obinata G, Dutta A. 2007, Vienna: ARS Press, 221-242."},{"key":"30_CR19","volume-title":"Pattern recognition and machine learning","author":"CM Bishop","year":"2006","unstructured":"Bishop CM: Pattern recognition and machine learning. 2006, Berlin: Springer"},{"key":"30_CR20","volume-title":"PHYLIP phylogeny inference package, Version 36","author":"M Felsenstein","year":"2004","unstructured":"Felsenstein M: PHYLIP phylogeny inference package, Version 36. 2004"},{"key":"30_CR21","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1109\/JPROC.2004.840301","volume":"93","author":"M Frigo","year":"2005","unstructured":"Frigo M, Johnson SG: The design and implementation of FFTW3. Proc IEEE. 2005, 93: 216-231.","journal-title":"Proc IEEE"},{"key":"30_CR22","first-page":"35","volume-title":"47th American Society for Cell Biology Meeting; Washington, DC","author":"L Shamir","year":"2007","unstructured":"Shamir L, Eckley DM, Goldberg IG: Image tiling vs. cell segmentation \u2013 a case study. 47th American Society for Cell Biology Meeting; Washington, DC. 2007, 35."},{"key":"30_CR23","first-page":"496","volume":"2","author":"L Shamir","year":"2006","unstructured":"Shamir L: Human perception-based color segmentation using fuzzy logic. Intl Conf on Image Processing, Computer Vision and Pattern Recognition. 2006, 2: 496-505.","journal-title":"Intl Conf on Image Processing, Computer Vision and Pattern Recognition"},{"key":"30_CR24","first-page":"1242","volume-title":"3rd Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining; Santa Barbara, CA","author":"DM Eckley","year":"2008","unstructured":"Eckley DM, Shamir L, Macura T, Orlon N, Goldberg IG: Automated quantitative analysis of phenotype similarities. 3rd Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining; Santa Barbara, CA. 2008, 1242."},{"key":"30_CR25","first-page":"1240","volume-title":"3rd Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining; Santa Barbara, CA","author":"L Shamir","year":"2008","unstructured":"Shamir L, Macura T, Orlov N, Eckley DM, Goldberg IG: IICBU 2008 \u2013 A benchmark suite for biological imaging. 3rd Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining; Santa Barbara, CA. 2008, 1240."},{"key":"30_CR26","unstructured":"IICBU-2008. [\n                    http:\/\/ome.grc.nia.nih.gov\/iicbu2008\n                    \n                  ]"},{"key":"30_CR27","unstructured":"Open Microscopy Environment. [\n                    http:\/\/www.openmicroscopy.org\n                    \n                  ]"},{"key":"30_CR28","unstructured":"Wndchrm download page. [\n                    http:\/\/www.phy.mtu.edu\/~lshamir\/downloads\/ImageClassifier\n                    \n                  ]"},{"key":"30_CR29","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1196\/annals.1310.013","volume":"1020","author":"RF Murphy","year":"2004","unstructured":"Murphy RF: Automated interpretation of protein subcellular location patterns: implications for early detection and assessment. Annals of the New York Academy of Sciences. 2004, 1020: 124-131.","journal-title":"Annals of the New York Academy of Sciences"},{"key":"30_CR30","volume-title":"British Machine Vision Conference","author":"I France","year":"1997","unstructured":"France I, Duller AWG, Lamb HF, T DGA: A comparative study of approaches to automatic pollen identification. British Machine Vision Conference. 1997"},{"key":"30_CR31","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1002\/(SICI)1097-0320(19981101)33:3<366::AID-CYTO12>3.0.CO;2-R","volume":"33","author":"M Boland","year":"1998","unstructured":"Boland M, Markey M, Murphy RF: Automated recognition of patterns characteristic of subsellular structures in florescence microscopy images. Cytometry. 1998, 33: 366-375.","journal-title":"Cytometry"},{"key":"30_CR32","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1093\/bioinformatics\/17.12.1213","volume":"17","author":"MV Boland","year":"2001","unstructured":"Boland MV, Murphy RF: A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics. 2001, 17: 1213-1223.","journal-title":"Bioinformatics"}],"container-title":["Source Code for Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1751-0473-3-13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1751-0473-3-13\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1751-0473-3-13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T20:21:07Z","timestamp":1548102067000},"score":1,"resource":{"primary":{"URL":"https:\/\/scfbm.biomedcentral.com\/articles\/10.1186\/1751-0473-3-13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,7,8]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["30"],"URL":"https:\/\/doi.org\/10.1186\/1751-0473-3-13","relation":{},"ISSN":["1751-0473"],"issn-type":[{"value":"1751-0473","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,7,8]]},"article-number":"13"}}