Crop a signal
Crop a signal using graphical interface.
LIP operations between images
Defined in 1985 by Michel Jourlin, the LIP Model (Logarithmic Image Processing) is a mathematical and physical framework dedicated to image processing. First defined as a framework adapted to images acquired in transmitted light, the interest of using LIP operators in a reflected light model has then been...
Negative
Compute the negative of an 8-bit grayscale image or volume.
Extraction of connected components in individual files, 2D and 3D
Extract, separate and save connected components in individual images/volumes in a directory. Can also be used to extract objects of interest from grayscale images/volumes from a binary mask. Update 20240820: added background value selection for images. Update 20230227: added support of 3D volumes. Update...
Overlay signals
Visualize and compare several signals by transparency display. Each signal can be translated and loaded independently.
CPE Lyon Morphological Random Models : introduction, course, 2019
CPE Lyon Morphological Random Models : introduction, course, 2019
LIP basic operators
Defined in 1985 by Michel Jourlin, the LIP Model (Logarithmic Image Processing) is a mathematical and physical framework dedicated to image processing. First defined as a framework adapted to images acquired in transmitted light, the interest of using LIP operators in a reflected light model has then been...
Robust tracking of an object of interest
Robust tracking of an object on a list of images. This plugin tracks an object of interest defined by a box on a list of images, and produces overlayed boxes or registrated images. It could be used in the case of noisy or very low contrasted images like TEM HR images. This plugin was used in the context of the ANR...
Get plane
Extract cut plane(s) of a volume. Update 20210223: add atlas extraction and extraction of all cut planes along one axis can be saved in TIFF or PNG format. Update 20200423: extraction of all cut planes along one axis.
Homogenization Dielectric Permittivity FFT scheme
An efficient method to solve the problem of homogenization of physical properties of heterogeneous media, such as dielectric permittivity, is the implementation of numerical solutions, before estimating the effective properties by spatial average of the solution. The input data is a 3D binary volume or a 2D binary...
Stereo reconstruction with Top-Down Segmented Regression
TDSR (Top-Down Segmented Regression) provides a stereo reconstruction method able to estimate the topography from SEM images. Standard stereo methods fail to evaluate adequate 3D reconstructions because of the homogeneous surface of these samples. The main approach of TDSR is to combine existing stereo methods with...
Histogram 2D/3D
Compute the histogram of an image or a volume. Updates 20230711: Support for unsigned char, integer, float, double types. Support for volume format.
Signal auto smoothing
The classical approaches of noise reduction do not adapt well to the variety of signals that can be encountered for different analysis methods (chromatography, XRD, Raman ...). The parameterization of these methods is often complex, with many parameters not very explicit or not intuitive and to be adapted according to...
SAXS for Boolean models of spheres
This plugin computes the scattering intensity from the analytical covariance of multiscale models built from union and intersection of Boolean models of spheres with Gamma or lognormal radius distributions. Another numerical approach, using projections of realisations for any kind of models, can be find in Sorbier et...
Deterministic M-tortuosity
Deterministic version of the M-tortuosity with imposed starting points set, for the characterization of 2D images and 3D volumes. Real images can be described now, obtained using electron tomography for instance. More details can be found using the links below. 22/02/22: bug correction 19/11/21: gathering of 2D...
Deleting spikes
Isolated aberrant point suppression. This plugin uses a h-maxima operator, called also contrast opening, from mathematical morphology.
Extract ROI from binary mask
Extract the region of interest (ROI) of an image using a binary image (supported formats are .bmp, .png, .jpg, .tiff, and .fda). The region of interest is extracted within a new image of the same size as the original image. Outside the region of interest, the intensity values are zero. Zero intensity values from the...
Local orientation estimation
Fast and robust method to estimate local orientations from the covariance matrix of the gradient. The estimation of the local orientation requires to define a size of neighbourhood around each pixel that contain several oriented objects. If you use this plugin, please cite : D. Jeulin, M. Moreaud. Segmentation of...
ARFBF Morphological Analysis
In the case of active phases observable in the form of stacked sheets, the classic strategy is to segment these sheets individually and characterize their length or curvature [Celse, 2008], which may related to actibity [Gandubert, 2006]. Since the images are quite noisy at this level of resolution, this type of...
Luminosity drift correction by morphological approach
Luminosity drift correction by TopHat operation combined with smoothing filter and / or LIP substraction.
Edge-preserving filter
Noise reduction of a grayscale image preserving the sharp edges of objects. Is based initially on the work of Kuwahara, then Schulze and Pearce. In contrast to the latter, which retain for a given point, the local mean of the lowest variance, a linear combination of the local means in the vicinity is held according to...
Projection
Orthogonal projection of a volume along x-axis, y-axis, or z-axis. This plugin can compute also opaque projection.
H-tortuosity-by-iterative-erosions
H-tortuosity-by-iterative-erosions for the characterization of 2D images and 3D volumes: Computation of the H-tortuosity estimator of the microstructure, as seen by a spherical particle of given size. In addition to keeping the properties of the H-tortuosity, this descriptor is linked to the notion of constrictivity,...
Resize image and volume by splines interpolation
Image and volume resizing by splines interpolation. See Biomedical Imaging Group of Ecole Polytechnique Fédérale de Lausannne (EPFL) for a very good tutorial concerning advanced uses of splines for image processing. Updates: 20240107: added volume resizing. 20210902: added interpolation mode, nearest-neighbor...
GCxGC/VUV advanced data processing
Comprehensive two-dimensional Gas Chromatography with Vacuum Ultraviolet detection (GC×GC/VUV) results in sizable data for which noise and baseline drift ought to be corrected. As GC×GC/VUV signal is acquired from multiple channels, these processing steps have to be applied from all channels while being robust and...
LIP edge detection
Defined in 1985 by Michel Jourlin, the LIP Model (Logarithmic Image Processing) is a mathematical and physical framework dedicated to image processing. First defined as a framework adapted to images acquired in transmitted light, the interest of using LIP operators in a reflected light model has then been...
BM3D Block matching and 3D filtering
BM3D (Block matching and 3D filtering) [1] is still today a reference algorithm for noise reduction. It is based on a splitting of the image into patches, a grouping of similar patches, a 2D filter in the patch domain, a 1D filter in the similarity domain, and then an inversion of these filters to reconstruct the...
Rugosity analysis
Rugosity / texture analysis by H-maxima and area of influences on zones of interest drawn over the image. Computation of local maxima or minima, then area of influence, and for each area of influence, extraction of the surface area, minimum, and maximum intensity values. The zones of interest are directly defined by...
Extract patches from image
Extract patches from image using graphical interface. Update: 200200923: adding normalization for 8 bits or 24bits RGB image.
Read NMR 2D text file
Compute a NMR 2D image from a text file exported from Bruker TopSpin software.