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 30 articles )

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  1. Boudina, Mouad; Gosselin, Frédérick P.; Étienne, Stéphane: Vortex-induced vibrations: a soft coral feeding strategy? (2021)
  2. Čapek, Martin; Blažíková, Michaela; Novotný, Ivan; Chmelová, Helena; Svoboda, David; Radochová, Barbora; Janáček, Jiří; Horváth, Ondrej: The wavelet-based denoising of images in Fiji, with example applications in structured illumination microscopy (2021)
  3. Frigau, Luca; Conversano, Claudio; Mola, Francesco: Consistent validation of gray-level thresholding image segmentation algorithms based on machine learning classifiers (2021)
  4. Gabitto, Mariano I.; Marie-Nelly, Herve; Pakman, Ari; Pataki, Andras; Darzacq, Xavier; Jordan, Michael I.: A Bayesian nonparametric approach to super-resolution single-molecule localization (2021)
  5. Kawamura, Mari; Sugihara, Kei; Takigawa-Imamura, Hisako; Ogawa, Toshiyuki; Miura, Takashi: Mathematical modeling of dynamic cellular association patterns in seminiferous tubules (2021)
  6. Kowal, Marek; Skobel, Marcin; Gramacki, Artur; Korbicz, Józef: Breast cancer nuclei segmentation and classification based on a deep learning approach (2021)
  7. Tiger Cross; Rasika Navarange; Joon-Ho Son; William Burr; Arjun Singh; Kelvin Zhang; Miruna Rusu; Konstantinos Gkoutzis; Andrew Osborne; Bart Nieuwenhuis: Simple RGC: ImageJ Plugins for Counting Retinal Ganglion Cells and Determining the Transduction Efficiency of Viral Vectors in Retinal Wholemounts (2021) not zbMATH
  8. Wenzel, Dennis; Nestler, Michael; Reuther, Sebastian; Simon, Maximilian; Voigt, Axel: Defects in active nematics - algorithms for identification and tracking (2021)
  9. Agosti, A.; Marchesi, S.; Scita, G.; Ciarletta, Pasquale: Modelling cancer cell budding in-vitro as a self-organised, non-equilibrium growth process (2020)
  10. 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)
  11. Halim, Abdul; Kumar, B. V. Rathish: A (TV-L^2-H^-1) PDE model for effective denoising (2020)
  12. Joshua C. Peterson, Marco C. DeRuiter: Fluorescent Nuclei Measurements Macro (FNMM), a tool for automated cell quantification in ImageJ (2020) not zbMATH
  13. An, Feng-Ping; Liu, Zhi-Wen: Image processing algorithm based on bi-dimensional local mean decomposition (2019)
  14. Ciocanel, Maria-Veronica; Sandstede, Bjorn; Jeschonek, Samantha P.; Mowry, Kimberly L.: Modeling microtubule-based transport and anchoring of mRNA (2018)
  15. 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)
  16. 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)
  17. Joseph C. Ferguson, Francesco Panerai, Arnaud Borner, Nagi N. Mansour: PuMA: the Porous Microstructure Analysis software (2018) not zbMATH
  18. Richard Beare; Bradley Lowekamp; Ziv Yaniv: Image Segmentation, Registration and Characterization in R with SimpleITK (2018) not zbMATH
  19. 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)
  20. Cwikel, Michael; Frazier, Michael; Jawerth, Louise M.; Milman, Mario: Björn David Jawerth (1952--2013) (2017)

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