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.
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...
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...
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 “...
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...
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...
Segmentation and detection of overlapped ellipses in binary images
This plugin proposes a complete method for recognizing and measuring highly overlapping ellipses in binary images. Starting from a binary image (the ellipses to be detected must be white on a black background), the pattern recognition process consists of the following successive steps: i) identification of all the...
M-tortuosity
Computation of the M-tortuosity estimator for the characterization of 2D images and 3D volumes: a scalable topological descriptor providing a 3D map of mean tortuosities, a set of M-coefficients, of which the histogram is meaningful, and a final scalar value, the M-scalar, assessing the geometric tortuosity of the...
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...
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 FDA, BMP, JPEG or TIFF format. Images are taken in alphabetical order. The result is a 3D volume. Update 20211029 : support for FDA format. Update 20191118 : support for BMP and JPEG images...
Batch processing
Do batch processing of all files of a directory without a single line of code.
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...
Border kill
Binary border kill morphological operation. Delete all connected components that touch the border of the image.
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...
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...
Mathematical morphology binary geodesic operations 2D and 3D
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 are...
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...
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
M-tortuosity-by-iterative-erosions
M-tortuosity-by-iterative-erosions for the characterization of 2D images and 3D volumes: Computation of the M-tortuosity estimator of the microstructure, as seen by a spherical particle of given size. In addition to keeping the properties of the M-tortuosity, this descriptor is linked to the notion of constrictivity,...
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.
3D surface area
3D surface area measurement of object(s) inside a volume. Each connected components can be consider as one object, or the entire volume as only one object. The calculation is from [Lindblad, 2005] : the estimation is performed with a “marching cube” approach using local weights. Two kind of local weights are...
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...
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.
Granulometry by morphological opening by disks
Morphological opening granulometry with increasing radius disks for binary images.
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.
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. Update 20210504 : analysis of the largest connected...
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.
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...
Workshop GdR NanOperando 2019
A workshop dedicating to the potential of plug im! platform to extract quantitative information from data from in situ experiments, therefore "dynamic" by nature! Includes a package with a set of plug im! modules, working data files, and pdf slides to guide users.
Criterion opening
Opening by criterion, usually referred to as attribute opening (Breen & Jones, 1996; Serra, 1988; Walter, 2003; Salembier et al., 1998) is a class of more general connected filters (Salembier&Wilkinson, 2009). In binary context, this operation is a filter on the set of the connected components (CC) based on criterion...