Add-ons for DIPimage

Most of the add-ons here require DIPimage 2.9, and might not work with the latest release. You can download DIPimage 2.9 through this page.

• Calibration photon counts from a single image.
  Reference: R. Heintzmann, P.K. Relich, P.P.J. Nieuwenhuizen, K.A. Lidke, B. Rieger, submitted

• Deconvolution methods for structured illumination microscopy.
  Reference: N. Chakrova, B. Rieger, S. Stallinga, Deconvolution methods for structured illumination microscopy, Journal of the Optical Society of America A, 33(7):B12-B20, 2016.

• Co-orientation.
  Reference: R.P.J. Nieuwenhuizen, L. Nahidi Azar, E.M.M. Manders, K. Jalink, Stallinga, B. Rieger, Co-orientation: Quantifying simultaneous co-localization and orientational alignment of filaments in light microscopy, PLoS ONE, 10(7):e0131756, 2015.

• Quantitative localization microscopy.
  Reference: R.P.J. Nieuwenhuizen, M. Bates, A. Szymborska, K.A. Lidke, B. Rieger, S. Stallinga, Quantitative localization microscopy: Effects of photophysics and labeling stoichiometry, PLoS ONE, 10(5):e0127989, 2015.

• Image Resolution.
  Reference: R.P.J. Nieuwenhuizen, K.A. Lidke, M. Bates, D. Leyton Puig, D. Grünwald, S. Stallinga, B. Rieger, Measuring Image Resolution in Optical Nanoscopy, Nature Methods, 10(6):557-562, 2013.

• Podosome counting.
  Reference: M.B.M. Meddens, B. Rieger, C.G. Figdor, A. Cambi, K. van den Dries, Automated podosome identification and characterization in fluorescence microscopy images, Microscopy and Microanalysis, 19(1):180-189, 2013.

• CTF correction and forward modeling toolbox (send email to bernd@diplib.org).
  Reference: L.M. Voortman, E.M. Franken, L.J. van Vliet and B. Rieger, Fast, spatially varying CTF correction in TEM, Ultramicroscopy, 118:26-34, 2012.

• Defocus and Astigmatism Estimation (send email to bernd@diplib.org).
  Reference: M.Vulović, E.M. Franken, R.B.G. Ravelli, L.J. van Vliet, and B. Rieger, Precise and Unbiased Estimation of Astigmatism and Defocus in Transmission Electron Microscopy, Ultramicroscopy, 116:115-134, 2012.

• Single emitter fitting.
  Reference: C.S. Smith, N. Joseph, B. Rieger and K.A. Lidke, Fast, single-molecule localization that achieves theoretically minimum uncertainty, Nature Methods, 7(5):373-375, 2010.

• TEM CCD camera characterization add-on.
  Reference: M. Vulović, B. Rieger, L.J. van Vliet, A.J. Koster and R.B.G. Ravelli, A Toolkit for the Characterization of CCD cameras for Transmission Electron Microscopy, Acta Crytallographica D., 66:97-109, 2010.

• DNA analysis software add-on.
  Reference: F.G.A. Faas, B. Rieger, L.J. van Vliet and D.I. Cherny, DNA deformations near charged surfaces: electron and atomic force microscopy views, Biophysical Journal 97(4):1148-1157, 2009.

• PointCloudToolbox, for analysing 3D expresion patterns in fruit fly embryos (broken link, the US government pays money for research and requires the results to be freely available, but doesn’t pay money to keep the websites up).
  Reference: C.L. Luengo Hendriks, S.V.E. Keränen, C.C. Fowlkes, L. Simirenko, G.H. Weber, A.H. DePace, C.N. Henriquez, D.W. Kaszuba, B. Hamann, M.B. Eisen, J. Malik, D. Sudar, M.D. Biggin and D.W. Knowles, 3D morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline, Genome Biology 7:R123, 2006.