Find here my public softwares.
ImageJ
Chromatic aberrations correction in confocal microscopy
Despite modern confocal microscopes are diffraction limited, chromatic aberrations might be critical for the study of small structures (typically near maximal resolution). With the help of micro-beads, the chromatic shift field can be reconstructed and used to correct such artefact in images.
See attached document: user manual.
Non-local means denoising for biological images
Two of the limiting factor of fluorescent microscopy of alive embryos is the amount of light available and the efficiency of the fluorescent marker. The resulting images are usually noisy that can be removed by an appropriate modeling of the noise and an efficient denoising algorithm.
See attached document: user manual.
Illumination bias correction in electron microscopy images of mouse's embryos
One major acquisition artefact of electron microscopy is the illumination bias. Since in cells electron microscopy images there is no regions of homogeneous intensities, the classical correction methods cannot be applied. Instead, a constrained modeling of the illumination over the whole field of view is used.
See attached document: user manual.
Baby Brain Toolkit (BTK)
Baby Brain Toolkit (BTK)
BTK is a collections of open-source command-line programs (main applications and utilities) that are used for image processing of MRI fetal brain images. My contributions to this project are mainly about neural network reconstruction, developmental trajectory modeling and cortical features selection. See GitHub repository.
See references: Rousseau 2013; Rousseau 2011.
KDE / Linux
Digikam
Digikam is an open-source advanced photography management and editor. My contributions to this software are mainly about image processing, such as plug-ins for smart scaling and for local contrast adjustments. See Digikam's website.
