Software for RNA-seq analyses, and contributions to GTEx pipelines are available at github.com/francois-a.
The software that accompanies Aguet et al., Dev. Cell, 2013, is available from the LCCB website.
Software for the detection of diffraction-limited point sources in noisy data. The detection is based on a Gaussian approximation of the microscope point spread function and comprises two steps: an initial pass that generates a mask of pixels with significant intensity, followed by sub-pixel localization at local maxima within this mask.
Version 1.01 — 09.I.2014
F. Aguet, C.N. Antonescu*, M. Mettlen*, S.L. Schmid, and G. Danuser, "Advances in Analysis of Low Signal-to-Noise Images Link Dynamin and AP2 to the Functions of an Endocytic Checkpoint," Dev. Cell, 26(3), pp. 279-291, 2013.
See Supplemental Information for a detailed description of the algorithm.
Matlab software for the modeling and detection of point spread functions generated by fluorescent dipoles. The dipole model is steerable, allowing for rapid detection of dipole patterns in an image through a filter-based approach.
Version 1.02 — 08.IX.2014
F. Aguet, S. Geissbühler, I. Märki, T. Lasser, and M. Unser, "Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters," Opt. Express, 17(8), pp. 6829-6848, 2009. [pdf]
Matlab MEX implementations of vectorial1 and scalar2 point spread function models.
Version 1.01 — 31.VII.2013
 F. Aguet, S. Geissbühler, I. Märki, T. Lasser, and M. Unser, "Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters," Opt. Express, 17(8), pp. 6829-6848, 2009. [pdf]
 S.F. Gibson and F. Lanni, "Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy," J. Opt. Soc. Am. A, 8(10), pp. 1601-1613, 1991.
Steerable filters are computationally highly efficient filters for edge and line detection. The filters implemented here were optimized for improved orientation selectivity and are based on linear combinations of up to 5th order Gaussian derivatives.
Version 1.03 — 29.XI.2012
SteerableJ: version 1.12 — 09.I.2012 (key changes: stack processing added)
IJtools: version 1.02 — 09.I.2012
M. Jacob and M. Unser, "Design of Steerable Filters for Feature Detection Using Canny-Like Criteria," IEEE Trans. Pattern Anal. Mach. Intell., 26(8), pp. 1007-1019, 2004. [pdf]
Filters for the detection of curvilinear and surface features in 3-D.
Version 1.01 — 28.VIII.2012
F. Aguet, M. Jacob, M. Unser, "Three-Dimensional Feature Detection Using Optimal Steerable Filters," Proc. 2005 IEEE International Conference on Image Processing (ICIP'05), pp. II 1158-1161. [pdf].