Fiji: an open-source platform for biological-image analysis. Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities

References in zbMATH (referenced in 23 articles )

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  1. Boudina, Mouad; Gosselin, Frédérick P.; Étienne, Stéphane: Vortex-induced vibrations: a soft coral feeding strategy? (2021)
  2. Kawamura, Mari; Sugihara, Kei; Takigawa-Imamura, Hisako; Ogawa, Toshiyuki; Miura, Takashi: Mathematical modeling of dynamic cellular association patterns in seminiferous tubules (2021)
  3. Agosti, A.; Marchesi, S.; Scita, G.; Ciarletta, Pasquale: Modelling cancer cell budding in-vitro as a self-organised, non-equilibrium growth process (2020)
  4. Hahn, Artur; Bode, Julia; Krüwel, Thomas; Kampf, Thomas; Buschle, Lukas R.; Sturm, Volker J. F.; Zhang, Ke; Tews, Björn; Schlemmer, Heinz-Peter; Heiland, Sabine; Bendszus, Martin; Ziener, Christian H.; Breckwoldt, Michael O.; Kurz, Felix T.: Gibbs point field model quantifies disorder in microvasculature of U87-glioblastoma (2020)
  5. Halim, Abdul; Kumar, B. V. Rathish: A (TV-L^2-H^-1) PDE model for effective denoising (2020)
  6. An, Feng-Ping; Liu, Zhi-Wen: Image processing algorithm based on bi-dimensional local mean decomposition (2019)
  7. Ciocanel, Maria-Veronica; Sandstede, Bjorn; Jeschonek, Samantha P.; Mowry, Kimberly L.: Modeling microtubule-based transport and anchoring of mRNA (2018)
  8. Cooper, Laura J.; Zeller-Plumhoff, B.; Clough, G. F.; Ganapathisubramani, B.; Roose, T.: Using high resolution X-ray computed tomography to create an image based model of a lymph node (2018)
  9. de La Fuente Canto, C.; Kalogiros, D. I.; Ptashnyk, M.; George, T. S.; Waugh, R.; Bengough, A. G.; Russell, J.; Dupuy, Lionel X.: Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach (2018)
  10. Joseph C. Ferguson, Francesco Panerai, Arnaud Borner, Nagi N. Mansour: PuMA: the Porous Microstructure Analysis software (2018) not zbMATH
  11. Richard Beare; Bradley Lowekamp; Ziv Yaniv: Image Segmentation, Registration and Characterization in R with SimpleITK (2018) not zbMATH
  12. Cooper, L. J.; Daly, K. R.; Hallett, P. D.; Naveed, M.; Koebernick, N.; Bengough, A. G.; George, T. S.; Roose, T.: Fluid flow in porous media using image-based modelling to parametrize Richards’ equation (2017)
  13. Cwikel, Michael; Frazier, Michael; Jawerth, Louise M.; Milman, Mario: Björn David Jawerth (1952--2013) (2017)
  14. Escande, Paul; Weiss, Pierre; Zhang, Wenxing: A variational model for multiplicative structured noise removal (2017)
  15. Jawerth, Louise M.; Weitz, David A.: Tracking the structural deformation of a sheared biopolymer network (2017)
  16. Keyes, Samuel David; Zygalakis, Konstantinos C.; Roose, Tiina: An explicit structural model of root hair and soil interactions parameterised by synchrotron X-ray computed tomography (2017)
  17. Yates, Christian A.; Ford, Matthew J.; Mort, Richard L.: A multi-stage representation of cell proliferation as a Markov process (2017)
  18. Cooper, Laura J.; Heppell, James P.; Clough, Geraldine F.; Ganapathisubramani, Bharathram; Roose, Tiina: An image-based model of fluid flow through lymph nodes (2016)
  19. Daerr, A.; Mogne, A.: Pendent_Drop: An ImageJ Plugin to Measure the Surface Tension from an Image of a Pendent Drop (2016) not zbMATH
  20. Korvin, Gabor: Permeability from microscopy: review of a dream (2016)

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