Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
10.1038/nprot.2014.037
Crossref journal-article
Springer Science and Business Media LLC
Nature Protocols (297)
Bibliography

Rizk, A., Paul, G., Incardona, P., Bugarski, M., Mansouri, M., Niemann, A., Ziegler, U., Berger, P., & Sbalzarini, I. F. (2014). Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3), 586–596.

Authors 9
  1. Aurélien Rizk (first)
  2. Grégory Paul (additional)
  3. Pietro Incardona (additional)
  4. Milica Bugarski (additional)
  5. Maysam Mansouri (additional)
  6. Axel Niemann (additional)
  7. Urs Ziegler (additional)
  8. Philipp Berger (additional)
  9. Ivo F Sbalzarini (additional)
References 38 Referenced 221
  1. Sbalzarini, I.F. Modeling and simulation of biological systems from image data. Bioessays 35, 482–490 (2013). (10.1002/bies.201200051) / Bioessays by IF Sbalzarini (2013)
  2. Adler, J. & Parmryd, I. Quantifying colocalization by correlation: the Pearson correlation coefficient is superior to the Mander's overlap coefficient. Cytometry A. 77, 733–742 (2010). (10.1002/cyto.a.20896) / Cytometry A. by J Adler (2010)
  3. Bolte, S. & Cordelieres, F.P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006). (10.1111/j.1365-2818.2006.01706.x) / J. Microsc. by S Bolte (2006)
  4. Manders, E.M.M., Verbeek, F.J. & Aten, J.A. Measurement of co-localization of objects in dual-colour confocal images. J. Microsc. 169, 375–382 (1993). (10.1111/j.1365-2818.1993.tb03313.x) / J. Microsc. by EMM Manders (1993)
  5. Li, Q. et al. A syntaxin 1, Gαo, and N-type calcium channel complex at a presynaptic nerve terminal: analysis by quantitative immunocolocalization. J. Neurosci. 24, 4070–4081 (2004). (10.1523/JNEUROSCI.0346-04.2004) / J. Neurosci. by Q Li (2004)
  6. van Steensel, B. et al. Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons. J. Cell Sci. 109 (Part 4): 787–792 (1996). (10.1242/jcs.109.4.787) / J. Cell Sci. by B van Steensel (1996)
  7. Costes, S.V. et al. Automatic and quantitative measurement of protein-protein colocalization in live cells. J. Biophys. 86, 3993–4003 (2004). (10.1529/biophysj.103.038422) / J. Biophys. by SV Costes (2004)
  8. Ramirez, O., Garcia, A., Rojas, R., Couve, A. & Hartel, S. Confined displacement algorithm determines true and random colocalization in fluorescence microscopy. J. Microsc. 239, 173–183 (2010). (10.1111/j.1365-2818.2010.03369.x) / J. Microsc. by O Ramirez (2010)
  9. Helmuth, J.A., Paul, G. & Sbalzarini, I.F. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics 11, 372 (2010). (10.1186/1471-2105-11-372) / BMC Bioinformatics by JA Helmuth (2010)
  10. Bolte, S. & Cordelières, F.P. Reply to letter to the editor. J. Microsc. 227, 84–85 (2007). (10.1111/j.1365-2818.2007.01789.x) / J. Microsc. by S Bolte (2007)
  11. Zinchuk, V., Wu, Y., Grossenbacher-Zinchuk, O. & Stefani, E. Quantifying spatial correlations of fluorescent markers using enhanced background reduction with protein proximity index and correlation coefficient estimations. Nat. Protoc. 6, 1554–1567 (2011). (10.1038/nprot.2011.384) / Nat. Protoc. by V Zinchuk (2011)
  12. Danuser, G. Computer vision in cell biology. Cell 147, 973–978 (2011). (10.1016/j.cell.2011.11.001) / Cell by G Danuser (2011)
  13. Paul, G., Cardinale, J. & Sbalzarini, I.F. Coupling image restoration and segmentation: a generalized linear model/Bregman perspective. Int. J. Comput. Vis. 104, 69–93 (2013). (10.1007/s11263-013-0615-2) / Int. J. Comput. Vis. by G Paul (2013)
  14. Abramoff, M.D., Magalhães, P.J. & Ram, S.J. Image processing with ImageJ. Biophoton. Int. 11, 36–42 (2004). / Biophoton. Int. by MD Abramoff (2004)
  15. Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012). (10.1038/nmeth.2089) / Nat. Methods by CA Schneider (2012)
  16. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). (10.1038/nmeth.2019) / Nat. Methods by J Schindelin (2012)
  17. Paul, G., Cardinale, J. & Sbalzarini, I.F. An alternating split Bregman algorithm for multi-region segmentation. in Proc. 45th IEEE Asilomar Conf. Signals, Systems, and Computers 426–430 (Asilomar, 2011). (10.1109/ACSSC.2011.6190034)
  18. Helmuth, J.A. & Sbalzarini, I.F. Deconvolving active contours for fluorescence microscopy images. in Proc. Intl. Symp. Visual Computing (ISVC), vol. 5875 of Lecture Notes in Computer Science, 544–553 (Springer, 2009). (10.1007/978-3-642-10331-5_51)
  19. Cardinale, J., Paul, G. & Sbalzarini, I.F. Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process. 21, 3531–3545 (2012). (10.1109/TIP.2012.2192129) / IEEE Trans. Image Process. by J Cardinale (2012)
  20. Helmuth, J.A., Burckhardt, C.J., Greber, U.F. & Sbalzarini, I.F. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. J. Struct. Biol. 167, 1–10 (2009). (10.1016/j.jsb.2009.03.017) / J. Struct. Biol. by JA Helmuth (2009)
  21. R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2012).
  22. Shivanandan, A., Radenovic, A. & Sbalzarini, I.F. MosaicIA: An ImageJ/Fiji plug-in for spatial pattern and interaction analysis. BMC Bioinformatics 14, 349 (2013). (10.1186/1471-2105-14-349) / BMC Bioinformatics by A Shivanandan (2013)
  23. Eliceiri, K.W. et al. Biological imaging software tools. Nat. Methods 9, 697–710 (2012). (10.1038/nmeth.2084) / Nat. Methods by KW Eliceiri (2012)
  24. Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006). (10.1186/gb-2006-7-10-r100) / Genome Biol. by AE Carpenter (2006)
  25. Sommer, C., Straehle, C., Koethe, U. & Hamprecht, F.A. Ilastik: Interactive learning and segmentation toolkit. Genome Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on 10.1109/ISBI.2011.5872394 (IEEE, 2012).
  26. Sternberg, S.R. Biomedical image processing. Computer 16, 22–34 (1983). (10.1109/MC.1983.1654163) / Computer by SR Sternberg (1983)
  27. Chambers, J., Freeny, A. & Heiberger, R. Analysis of variance; designed experiments. in Statistical Models in S 145–193 (Wadsworth and Brooks/Cole Advanced Books and Software, 1992). (10.1201/9780203738535-5)
  28. Miller, J.R. Simultaneous Statistical Inference (Springer-Verlag, 1981). (10.1007/978-1-4613-8122-8)
  29. Sbalzarini, I.F. & Koumoutsakos, P. Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol. 151, 182–195 (2005). (10.1016/j.jsb.2005.06.002) / J. Struct. Biol. by IF Sbalzarini (2005)
  30. Linkert, M. et al. Metadata matters: access to image data in the real world. J. Cell Biol. 189, 777–782 (2010). (10.1083/jcb.201004104) / J. Cell Biol. by M Linkert (2010)
  31. Zhang, B., Zerubia, J. & Olivo-Marin, J.C. Gaussian approximations of fluorescence microscope point-spread function models. Appl. Opt. 46, 1819–1829 (2007). (10.1364/AO.46.001819) / Appl. Opt. by B Zhang (2007)
  32. Sönnichsen, B., De Renzis, S., Nielsen, E., Rietdorf, J. & Zerial, M. Distinct membrane domains on endosomes in the recycling pathway visualized by multicolor imaging of Rab4, Rab5, and Rab11. J. Cell Biol. 149, 901–914 (2000). (10.1083/jcb.149.4.901) / J. Cell Biol. by B Sönnichsen (2000)
  33. Ballmer-Hofer, K., Andersson, A.E., Ratcliffe, L.E. & Berger, P. Neuropilin-1 promotes VEGFR-2 trafficking through Rab11 vesicles thereby specifying signal output. Blood 118, 816–826 (2011). (10.1182/blood-2011-01-328773) / Blood by K Ballmer-Hofer (2011)
  34. Kriz, A. et al. A plasmid-based multigene expression system for mammalian cells. Nat. Commun. 1, 120 (2010). (10.1038/ncomms1120) / Nat. Commun. by A Kriz (2010)
  35. Matsuo, H. et al. Role of LBPA and Alix in multivesicular liposome formation and endosome organization. Science 303, 531–534 (2004). (10.1126/science.1092425) / Science by H Matsuo (2004)
  36. Fitzgerald, D.J. et al. Protein complex expression by using multigene baculoviral vectors. Nat. Methods 3, 1021–1032 (2006). (10.1038/nmeth983) / Nat. Methods by DJ Fitzgerald (2006)
  37. Niemann, A., Ruegg, M., La Padula, V., Schenone, A. & Suter, U. Ganglioside-induced differentiation associated protein 1 is a regulator of the mitochondrial network: new implications for Charcot-Marie-Tooth disease. J. Cell Biol. 170, 1067–1078 (2005). (10.1083/jcb.200507087) / J. Cell Biol. by A Niemann (2005)
  38. Ruusuvuori, P. et al. Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics 11, 248 (2010). (10.1186/1471-2105-11-248) / BMC Bioinformatics by P Ruusuvuori (2010)
Dates
Type When
Created 11 years, 6 months ago (Feb. 13, 2014, 11:39 a.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 8:16 p.m.)
Indexed 2 weeks, 3 days ago (Aug. 5, 2025, 8:59 a.m.)
Issued 11 years, 6 months ago (Feb. 13, 2014)
Published 11 years, 6 months ago (Feb. 13, 2014)
Published Online 11 years, 6 months ago (Feb. 13, 2014)
Published Print 11 years, 5 months ago (March 1, 2014)
Funders 0

None

@article{Rizk_2014, title={Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh}, volume={9}, ISSN={1750-2799}, url={http://dx.doi.org/10.1038/nprot.2014.037}, DOI={10.1038/nprot.2014.037}, number={3}, journal={Nature Protocols}, publisher={Springer Science and Business Media LLC}, author={Rizk, Aurélien and Paul, Grégory and Incardona, Pietro and Bugarski, Milica and Mansouri, Maysam and Niemann, Axel and Ziegler, Urs and Berger, Philipp and Sbalzarini, Ivo F}, year={2014}, month=feb, pages={586–596} }