Add-ons

This page provides links to

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 the link on the side-bar.

• 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. 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.

• Granulometries. Reference: C.L. Luengo Hendriks, G.M.P. van Kempen and L.J. van Vliet, Improving the accuracy of isotropic granulometries, Pattern Recognition Letters 28(7):865-872, 2007.

• Morphological operations with line structuring elements. Reference: C.L. Luengo Hendriks and L.J. van Vliet, Using line segments as structuring elements for sampling-invariant measurements, IEEE Transactions on Pattern Analysis and Machine Intelligence 27(11):1826-1831, 2005.

• Sampling-free morphological operations in 1D. Reference: C.L. Luengo Hendriks and L.J. van Vliet, Basic morphological operations, band-limited images and sampling, in: L.D. Griffin and M. Lillholm (eds.), Lecture Notes on Computer Science 2695:313-324, Springer, Berlin, 2003.