Open-source codes associated with the publications I co-authored.

Inverse Problems in Biomedical Imaging

	GlobalBioIm Library A Matlab library for solving inverse problems. [Code] [Paper] [Website]
	Structured Illumination Microscopy (SIM) FlexSIM A flexible SIM reconstruction method capable to handle difficult data prone to reconstruction artifacts. [Code] [Paper] Single-slice SIM Reconstruction algorithm enabling the estimation of the out-of-focus signal and based on an inner-loop-free ADMM. [Code] [Paper]
	Single Molecule Localization Microscopy (SMLM) Sliding Frank-Wolfe: Grid-less method that minimizes the BLASSO. [Code] [Paper] SMLM-CEL0: Grid-based method that relies on the minimization of the Continuous Exact L0 functional. [Code] [Paper] Continuous FRC: Computes the Fourier-ring correlation (FRC) in the continuous domain for single molecule localization microscopy. [Code] [Paper]
	Optical Diffraction Tomography (ODT) Reconstruction method based on the exact Lippmann-Schwinger forward model and the FISTA algorithm. [Code] [Paper Opt. Exp.] [Paper TCI]
	Multi-Angle Total Internal Reflection Fluorescence Microscopy (MA-TIRFM) Reconstruction algorithm that performs jointly volume reconstruction, deconvolution, and background estimation. [Code] [Paper Sci. Rep.] [Paper ISBI]
	Single-Particle Cryo Electron Microscopy (SP Cryo-EM) Joint angular refinement and reconstruction algorithm for single-particle Cryo-EM. [code] [Paper]

Sparse Optimization

	Safe screening with sphere refinement for sparse optimization Safe screening approach that exploits local strong concavity properties of the dual function to accelerate the convergence of iterative solvers. [Code] [Paper JMLR] [Paper SPL]
	Sliding Frank-Wolfe algorithm Grid-less method that minimizes the BLASSO. [Code] [Paper]
	L2 - CEL0 Minimization Examples of the use of the FBS and IRL1 algorithms to solve the CEL0 penalized least squares problem. [Code] [Paper SIOPT] [Paper SIIMS]

Non-negative Matrix Factorization (NMF)

Transform Learning NMF Illustrations of our paper on the identifiability of TL-NMF. [Code] [Paper] Comparisons between TL-NMF and Joint Diagonalization + NMF. [Code] [Paper]