Batch processing
Do batch processing of all files of a directory without a single line of code.
Extract profile from image and volume
Use graphical interface to extract horizontal of vertical profile. Move the line overlay on the image using the right mouse button. There are two modules: one for vertical profiles and one for horizontal profiles. Update 20211029 : adding profil extraction for 3D volume.
Compute under mask
Compute the mean, the max, the sum and the standard deviation for the zones defined by a mask. The zones are defined by a binary image (intensity 0 for background). This plugin can be used to compute integration of peaks with 2D data.
Drawing
Allows drawing over an image. Can be used to define a binary mask. It can also be used to modify an existing binary mask. Update 20190507 : adding the modification of an existing binary mask
Read NMR 2D text file
Compute a NMR 2D image from a text file exported from Bruker TopSpin software.
3D histogram automatic segmentation
This plugin offers image segmentation algorithms for 3D volume using a global approach based on the histogram. Depending on the application and the type of image, several criteria are available to detect many objects of interest [Otsu, 1979] [Diday, 1971] [Dempster, 1987] or few objects [Kapur, 1985] [ Huang, 1995]. A...
Mathematical morphology basic operations
Mathematical morphology has been introduced by Matheron and Serra [Serra, 1982] in the late 1960's. It defines among others, two basic operators: dilation and erosion. These tools and their combinations are powerful and widespread for filtering and image analysis. For instance, operations such as opening, closing or...
Histogram automatic segmentation
This plugin offers image segmentation algorithms using a global approach based on the histogram. Depending on the application and the type of image, several criteria are available to detect many objects of interest [Otsu, 1979] [Diday, 1971] [Dempster, 1987] or few objects [Kapur, 1985] [ Huang, 1995]. A strategy to...
Boolean model of spheres
This plugin generates one-scale Boolean random models of spheres located on point of a Poisson Point Process. A specific algorithm uses an original construction method without representation on a voxel grid, which generates wide simulations with a low computational cost. If you use this plugin, please cite “...
Border kill
Binary border kill morphological operation. Delete all connected components that touch the border of the image.
Overlay signals
Visualize and compare several signals by transparency display. Each signal can be translated and loaded independently.
3D height visualization
Visualize 3D volume behind the current plane. The algorithm uses a fast distance transform and gradient trick to give the impression of 3D iso-surface visualization. These work is inspired by those of Luc Vincent (see below), adapted to the visualization of a 3D volume. Take the opportunity to take a look at the other...
Compare, background subtraction
Use this plugin to compare two images or two volumes. Update 20230307 : fixed volume comparison problem. Update 20220617 : added the possibility to compute background subtraction. Update 20211022 : added the possibility to shift the data to be compared. Update 20190409 : support for volumes larger than 2 147 483...
Deleting spikes
Isolated aberrant point suppression. This plugin uses a h-maxima operator, called also contrast opening, from mathematical morphology.
Crop an image
Crop an image using graphical interface. It is also possible to precisely define the position and size of the area to be cut. Updates: 20200923: adding normalization for 8 bits or 24bits RGB image. 20200424: bug correction if crop full image. 20190611: fixed a bug concerning selection outside the definition...
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...
Crop a signal
Crop a signal using graphical interface.
Resize image by splines interpolation
Image 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. Update 20210902 : added interpolation mode, nearest-neighbor interpolation.
Hole filling 2D and 3D
Morphological hole filling operation. Fills all the holes of the connected components of the image, except for the holes that touch the border. Update 20220218 : added support for 3D volumes.
Box filter
Local mean filter using summed area tables* for computation with o(1) complexity. *F. C. Crow, “Summed-area tables for texture mapping,” in Proc. ACM SIGGRAPH, 1984, pp. 207–212 Update: 20230912: addition of an iteration parameter. 20201204: support for image of type integer, float and double.
Sphero cylinders Boolean model
This plugin generates one-scale Boolean random models of sphero-cylinders i.e. random oriented sphero cylinders located on points of a Poisson Point Process. A specific algorithm subdivides the volume and uses the properties of the Poisson point process to reduce significantly the computation time and to obtain...
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...
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...
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...
Flowing bilateral filter 3D
The bilateral filter plays a key role in image processing applications due to its intuitive parameterization and its high quality filter result, smoothing homogeneous regions while preserving the edges of the objects. Considering the image as a topological relief, seeing pixel intensities as peaks and valleys, we...