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...

Flowing bilateral filter

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...

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...

Thickness analysis

Compute the thickness of the largest connected component of an image using distance functions and a watershed operator. As a result, this plugin provides a report in text format indicating the average, minimum, maximum and standard deviation of this thickness.

Separation of binary objects

This plugin performs a separation of fusionned/linked binary objects with standard approch from mathematical morphology i.e. using operators such as opening, distance transform, h-maxima, and watershed. For more explanations, look at Serge Beucher (PSL Mines ParisTech, CMM) courses, and take opportunity to read his...

Robust derivative of a signal

Compute robust derivative of a signal using self-adapting filtering. This plugins applies a filter on the initial data, compute the derivative, and can also applies a post filtering on the obtained derivative. The self-adapting filtering is based on the algorithm used on signal auto smoothing plugin.

Histogram under mask

Compute the gray level histogram for the zones defined by a mask. The zones are directly defined by drawing on the image (use the help button of the plugin to know more). This plugin computes also gray levels histogram of the union of the zones.

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...

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 tiff 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 TIFF format. Images are taken in alphabetical order. The result is a 3D volume with 8 bits intensity. Update 20190409 : support for volumes larger than 2 147 483 648 voxels.

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.


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...


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. Update 20180917 : adding the possibility to manually set coordinates. Update 20190510 : fixed a bug concerning selection outside the definition domain of the current image.

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.