Software Listing of Author : "David Legland"

usage : map = blue2red; colormap(blue2red); Returns a 256x3 array which can be used with colormap. map(1,:) corresponds to blue color, map(64,:) corresponds to cyan color, map(128,:) corresponds to green color, map(192,:) corresponds to yellow color, map(256,:) corresponds to red color, and all indices inbetween are gradient between the 2 extremes colors. Example colormap(blue2red);

  • Platform: Matlab, Scripts

Crofton Perimeter is a lightweight plugin for ImageJ designed to help you easily determine the Crofton perimeter of an opened label image.

Crofton Perimeter can be accessed from the Plugins menu of ImageJ. In order to calculate the perimeter, it prompts you to specify the input image and the number of directions.

  • Platform: WinOther

Computes the min and max values within the input array, convert to 256 values, and apply a colormap to produce a color image (RGB). It is possible to specifies the range of values to consider, as well as the background color (used for NaN values). Example: % Display a default matrix subplot(1, 2, 1); imshow(peaks(128), []); title('as double') % display the coresponding RGB image subplot(1, 2, 2); imshow(double2rgb(peaks(128), jet, [-8 8])); title('as RGB');

  • Platform: Matlab, Scripts

Fast Morphology is a plugin for ImageJ that enables you to apply several morphological filters to your pictures.

Fast Morphology provides support for multiple filters, including dilation, erosion, morphological gradient or laplacien. Additionally, you can use it to add borders to your image.

  • Platform: WinOther

Two functions for working with the Feret diameter of labelized particles in images. The function imFeretDiameter computes the Feret diameter for each one of the specified directions. The maximal diameter can be obtained by computing the max of the result. The function imOrientedBox computes Feret diameter for several directions, and keep the direction that produces the minimal-area enclosing rectangle. The function drawOrientedBox can be used for visualising result. Both functions could easily be adapted to a set of points.

  • Platform: Matlab, Scripts
  • geom2d
  • License: Shareware
  • Price:

Library to handle and visualize geometric primitives such as points, lines, circles and ellipses, polylines and polygons... The goal is to provide a low-level library for manipulating geometrical primitives, making easier the development of more complex geometric algorithms. The library proposes functions to: - create various shapes (points, circles, lines, ellipses, polylines, polygons) using an intuitive syntax. Ex: createCircle(p1, p2, p3) to create a circle through 3 points. - derive new shapes: intersection between 2 lines, between a line and a circle, parallel and perpendicular lines Functions to compute intersections - work on polylines and polygons: compute centroid and area, expand, clip with half-plane... - measure distances (between points, a point and a line, a point and a group of points), angle (of a line, between 3...

  • Platform: Matlab, Scripts

Contains various functions for measuring or estimating geometric quantities from 2D or 3D images. Parameters available for 2D images are: * the area (number of pixels) * the perimeter (based on Crofton formula) * the(2D) Euler Number Parameters available for 3D images are: * the volume, * the surface area (measured using the Crofton formula), * the mean breadth (also known as integral of mean curvature), * the (3D) Euler Number Most functions work both for binary and label images. It is possible to specify options (connectivity for Euler Number, number of directions for perimeter or surface area), as well as image resolution in each direction. For some parameters, it is also possible to estimate the density with respect to image area or volume. Example 1: measure perimeter in 2D label image lbl = bwlabel(imread('coins.png') >...

  • Platform: Matlab, Scripts

ijGeodesics is a lightweight and easy to use plugin for ImageJ that enables you to calculate the geodesic lengths for a label image.

Additionally, you can use it to determine the chamfer distance for each for a binary mask image. Besides the geodesic diameter, it also determines the radius of the particles.

  • Platform: WinOther

ijGranulometry provides you with a handy plugin for ImageJ that enables you to apply different grayscale morphological filters to your pictures.

There are two available filtering options: in radius or in diameter, as well as a batch filtering tool, which allows you to generate the granulometric curve graph for a set of images.

  • Platform: WinOther

The function "imInertiaEllipsoid" computes inertia coefficients of the 3D image, and returns the associated equivalent 3D ellipsoid. The function "drawEllipsoid" can be used to display result. The package also contains function imInertiaEllipse, that returns equivalent ellipse for 2D images. Results is similar to that obtained with IPT function regionprops, but with different output format. The result can be used directly with function 'drawEllipse'. Display of 3D image in the example requires the "slicer" contribution, also on FileExchange (ID 27983). Package includes functions from geom2d and geom3d contributions.

  • Platform: Matlab, Scripts

Generic function for computing histogram of an image. Image can be either 2D or 3D, grayscale or color. For color images, the result is the concatenation of the histogram computed for each band. If no output is requested, the histogram is plotted on the current axis. Several options can be applied, like min and max levels to consider, number of histogram bins, location of bin centers, region of interest. please send bug reports to author (david.legland at

  • Platform: Matlab, Scripts

Add a colored layer to a base image, whatever the dimension (2D or 3D) and the type (grayscale of color) of the base image. Overlays are given by pairs MASK + color. The mask is a binary image the same size as the base image. The color parameter can be either a rgb triplet (like [1 0 0] for red), or a color character (like 'g', 'w'...). It is also possible to specify another image as 'color', in this case the pixels of the base image within the mask will be replaced by the pixels of the 'color' image. The aim of this function was to be easy to use, without spending time in conversion between 2D/3D and color grayscale. Please send bug reports directly to authour (david dot legland at grignon dot inra dot fr).

  • Platform: Matlab, Scripts
  • javaGeom
  • License: Freeware
  • Price: 0.00

javaGeom is a Java library designed to help you develop geometry applications. The component provides a general framework for manipulating and creating geometric primitives, computing intersection points between shapes, composing them to create new shapes, and performing some measurements.

  • Platform: WinOther
  • Malimpa
  • License: Freeware
  • Price: 0.00

Malimpa, which is actually short for MAtlab Library for IMage Processing and Analysis is designed as a Matlab library.

It was designed in order to provide functions for 2D / 3D grayscale / color image creation, filtering, or measurement. It requires, and complements Matlab Image Processing Toolbox.

  • Platform: WinOther
  • matGeom
  • License: Freeware
  • Price: 0.00

matGeom is designed to be a Matlab library for geometric computing. Using the functions included in matGeom, you are able to create, transform, manipulate and display geometric primitives (points, lines, polygons, planes, etc.).

Typical operations involve creation of shapes, computation of intersections, transforming shape coordinates, combining shapes to create new ones. You can have a look at the demo pages to have an overview of the syntax and possibilities.

The library is organised into several packages:
· geom2d for general functions in the 2D euclidean plane,
· polygons2d for working with polylines and polygons,
· graphs for working on planar graphs,
· polynomialCurves2d that can be used for fitting geometric curves on set of points, typically after a coutour...

  • Platform: WinOther

Computes region adjacency graph of a labeled 2D or 3D image. Two regions are considered as neighbor if they are separated by a background (i. e. with color 0) pixel in the horizontal or vertical direction, as well as depth direction for 3D images. The result is a N*2 array, containing 2 indices for each couple of neighbor regions. usage: ADJ = imRAG(IMG); ADJ has the format [LBL1 LBL2], LBL1 and LBL2 being vertical arrays the same size. LBL1 is given in ascending order, LBL2 is given in ascending order for each LBL1. Ex : [1 2] [1 3] [1 4] [2 3] [2 5] [3 4] Alternative syntax: [NODES, ADJ] = imRAG(IMG); Return two arrays: the first one is a [N*2] array containing centroids of the N labeled region, and ADJ is the adjacency previously described. For 3D images, the node array is [N*3].

  • Platform: Matlab, Scripts
  • Slicer
  • License: Shareware
  • Price:

Simple interface for exploring 3D images by visualizing planar slices. It is not a 3D renderer, but allows to get a quick overview of the image. Among the interface features: - navigation within image, - zoom management, - edition of grayscale range (from datataype, from image, manual) - 3D image flip or 90-degrees rotation, - management of image resolution - import of metaimage, analyze or dicom images - display of 3 orthogonal slices, planar or 3D - management of several look-up tables It supports 3D grayscale, binary, RGB, or vector images (in this case, the vector norm is used for display). The package includes functions to read/write image stacks stored as tif slices or bundle, as well as basic support for reading and writing images in metaimage format (mhd). Examples of use: slicer(img); % display the 3D or 4D imge...

  • Platform: Matlab, Scripts
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