RNA-seq and eQTL analyses
Software for RNA-seq analyses, and contributions to GTEx pipelines are available at github.com/francois-a.
Software for analysis of clathrin-mediated endocytosis dynamics
The software that accompanies Aguet et al., Dev. Cell, 2013, is available from the LCCB website.
Fluorescent spot detection
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.
Matlab
Installation instructions:
- Download PointSourceDetection.zip.
- Decompress and add to Matlab path. The archive contains the source code, 64-bit
Os X , Linux, and Windows MEX binaries, and documentation.
Version 1.01 — 09.I.2014
Reference:
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.
Steerable model for fluorescent dipole PSFs
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.
Installation instructions:
- Download SteerableDipoles.zip.
- Decompress and add to Matlab path. The archive contains the source code, 64-bit Os X, Linux, and Windows MEX binaries, documentation, and example code.
Version 1.02 — 08.IX.2014
Reference:
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]
Microscope point spread function models
Matlab MEX implementations of vectorial1 and scalar2 point spread function models.
Installation instructions:
- Download PSFmodels.zip.
- Decompress and add to Matlab path. The archive contains the source code, 64-bit Os X, Linux, and Windows MEX binaries, documentation, and example code.
Version 1.01 — 31.VII.2013
References:
[1] 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]
[2] 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.
2-D Steerable filters for feature detection
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.
Matlab MEX-files
Installation instructions:
- Download SteerableDetector.zip.
- Decompress and add to Matlab path. Archive includes help file and 64-bit Os X, Linux, and Windows MEX binaries.
Version 1.03 — 29.XI.2012
ImageJ plug-in
Installation instructions:
- Download SteerableJ.zip and unzip it into the ImageJ "plugins" directory.
- Download the ijtools.jar package to the ImageJ/plugins/ directory.
- API Documentation: steerablej package; ijtools package.
SteerableJ: version 1.12 — 09.I.2012 (key changes: stack processing added)
IJtools: version 1.02 — 09.I.2012
Reference:
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]
3-D Steerable filters for feature detection
Filters for the detection of curvilinear and surface features in 3-D.
Matlab MEX-files
- Download SteerableDetector3D.zip
- Decompress and add files to Matlab path. Archive includes help file and 64-bit Os X, Linux, and Windows binaries.
Version 1.01 — 28.VIII.2012
Reference:
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].