Crop 3D object

Crop a volume using mouse interactions or with precise parameters. Update 20190219 : support for volumes with unsigned char, integer, float, double and complex intensities.

Granulometry by morphological opening by disks

Morphological opening granulometry with increasing radius disks for binary images.

3D volume from images list

Create a 3D volume from images listed in a directory. Simply load one of the images of the directory. Images should be in BMP, JPEG or TIFF format. Images are taken in alphabetical order. The result is a 3D volume with 8 bits intensity. Update 20191118 : support for BMP and JPEG images format. Update 20190409 :...

FACE : Fast mean Absolute difference with Confidence propagation for Extended depth of field

Bright field microscopes with low depth of field provide good magnification and image quality. However, samples generally have a thickness greater than the depth of field, thus being not entirely observable within the viewing distances intervals and preventing the creation of sharp images. It is possible to gradually...

Batch processing

Do batch processing of all files of a directory without a single line of code.

Extract profile from 2D image

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.

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

Use this plugin to compare two images or two volumes. Update 20190409 : support for volumes larger than 2 147 483 648 voxels.

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 : 20200424 : bug correction if crop full image. 20190611 : fixed a bug concerning selection outside the definition domain of the current image. 20180917 : adding the possibility...

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.

Hole filling

Morphological hole filling operation. Fills all the holes of the connected components of the image, except for the holes that touch the border.

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

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...