Analyzeparticles
Contents |
Purpose
ANALYZEPARTCLES Identify particles (blobs, connected regions), and their properties, in an image dataset.
Synopsis
- [imgdso, model] = analyzeparticles(x, options);
- [imgdso, model] = analyzeparticles(x);
- [imgdso, model] = analyzeparticles(x, model);
Description
Particle analysis is used to identify particle-like areas in an image and return information about the identified particles’ characteristics such as their area, shape and pixel values. A particle is considered to be an isolated contiguous region of pixels within the image which have similar intensity values or color values. Particles are also known as “connected regions” or “blobs”.
Our image analysis software can analyze particles in images using either the “analyzeparticles” Matlab function or the “Particle Analysis” GUI, which is a graphical interface to that function. The analyzeparticles function itself is implemented using the ImageJ image analysis package (http://rsb.info.nih.gov/ij/) which is included with our software. Analyzeparticles integrates the ImageJ “Analyze Particles” feature into our software so it can be conveniently used with the Eigenvector dataset object and the other MIA/PLS_Toolbox tools.
Inputs
- x = image dataset object with one or more slabs,
- model = previously generated model of type 'ANALYZEPARTICLES' (when applying model to new data).
Outputs
- imgdso = input imgdso modified with addition of classesets identifying particles. One classset has a class for each particle. Pixels within particle j have class = j. Non particle pixels have class = 0. Second classset has one class for all particles. Pixels within any particle have class = 1. Non particle pixels have class = 0.
- model = a standard model structure model with the following fields (see Standard Model Structure):
- modeltype: 'ANALYZEPARTICLES',
- datasource: structure array with information about input data,
- date: date of creation,
- time: time of creation,
- info: additional model information,
- particletable: A dataset containing the requested particle properties,
- Rows are particles,
- Columns represent properties, identified by particletable.label{2}.
- allparticles: a vector with one entry per pixel, value = 0 if pixel is not a particle pixel, 1 otherwise.
- particles: a vector with one entry per pixel, value = j, where j = 0, 1, ...n if pixel is part of particle number j.
- foreground: a vector with one entry per pixel, value = 0 or 255, showing the binary image representing all possible particle pixels.
- detail: sub-structure with additional model details and results, including:
- model.detail.thresholdValue: the threshold value used in forming the binary image,
- model.detail.height: height of the image (in pixels),
- model.detail.width: width of the image (in pixels),
- model.detail.nparticles: number of identified particles,
- model.detail.ij: contains the Java evri.ij.plugin.ParticlesAnalyzer object.
Options
options = a structure array with the following fields:
- display: [ 'off' | {'on'} ], governs level of display to command window. 'off' suppresses output,
- plots [ 'none' | {'final'} ], governs level of plotting,
- includeholes: [ 'off' | {'on'} ], holes within particles are included?,
- includeedgeparticles: [ {'off'} | 'on' ], include particles intersecting the image's edge?,
- thresholdslab: Index of dataset slab to use for creating binary image. Default = [],
- thresholdvalue: Value to use as threshold when creating binary image,
- reversemask: [ 'off' | {'on'}] reverse the particle binary mask? ('on' means find bright particles. See below).
- apply_abs: [ {'off'} | 'on' ] apply absolute value to data initially?
The following four options represent criteria which potential particles must satisfy to be considered particles:
- minsize: Lower limit to particle area. Default is 50 pixels,
- maxsize: Upper limit to particle area. Default is infinite,
- mincircularity: Lower limit to particle circularity. Default = 0.0,
- maxcircularity: Upper limit to particle circularity. Default = 1.0,
The remaining options indicate whether these additional particle properties should be measured and reported:
- particleminmax: [ {'off'} | 'on' ] measure particle min and max values,
- particlemedian: [ {'off'} | 'on' ] measure particle median value,
- particlestddev: [ {'off'} | 'on' ] measure particle standard deviation value,
- particleperimeter: [ {'off'} | 'on' ] measure length of particle perimeter (pixels),
- particleshape: [ {'off'} | 'on' ] measure particle shape parameters (Conc., AR, Round, Solidity),
- particleferet: [ {'off'} | 'on' ] measure Feret diameters of particle.
Algorithm
There are two steps to particle analysis of an image dataset object (DSO). The first step is to obtain a binary image where image pixel values are either 0 or 1 where one value represents non-particle pixels and the other represents potential particle pixels. This is usually accomplished by specifying a threshold level where pixels having a value below or above the threshold value are assigned value 0 or 1. If no threshold level is specified then one is automatically determined as in the ImageJ auto thresholding method. If the image DSO has multiple slabs then one slab must be selected to determine the binary image or else the average of all the slabs can be used. A pixel assigned value 1 is not automatically part of a particle because other particle criteria can be specified such as a minimum particle area requirement, or other shape restriction. Once these filters are applied there may remain some particle regions.
The second step in particle analysis is to calculate the properties of each particle region. Properties include area, perimeter, centroid coordinates, shape properties (circularity, aspect ratio, roundness, and solidity) and Feret’s diameters (Feret diameter, FeretX, FeretY, FeretAngle and MinFeret). There are other particle properties which depend on the particle’s pixel values including mean, median, minimum, maximum, and standard deviation. These are calculated for each slab for each particle.
Measured Particle Properties
Properties of each particle are returned in the model.particletable DSO. Particles' centroid coordinates (w, h) are always returned. Coordinates are given using the image convention where (x,y) indicates distance in pixels measured from the top left corner of the image, so the top left corner has coordinates (0,0) while the bottom right corner has coordinates (nwidth-1, nheight-1).
- X, Y are the coordinates of the particle's centroid.
Additional particle properties can be obtained by specifying options:
- Mean = mean pixel value over particle, per slab
- Median = mean pixel value over particle, per slab
- Min = minimum pixel value over particle, per slab
- Max = maximum pixel value over particle, per slab
- StdDev = standard deviation of pixel values over particle, per slab.
Particle properties which only depend on the particle shape (are the same for all slabs) include:
- Area = area of particle (in square pixels),
- Perim. = length of particle perimeter in pixel lengths.
Particle shape properties:
- Circ. (circularity = 4π*area/perimeter^2. A value of 1.0 indicates a perfect circle. As the value approaches 0.0, it indicates an increasingly elongated shape. Values may not be valid for very small particles. Also note that a circular particle with large holes will have smaller area than a circle with that perimeter, so circularity is only accurate if the particle has no holes (or 'includeholes=on'). A circular particle with large holes will have small solidity.
- AR (aspect ratio) = major_axis/minor_axis.
- Round (roundness) = 4*area/(π*major_axis^2), or the inverse of the aspect ratio.
- Solidity = area/convex area.
Particle Feret diameters, Feret's Diameter is the longest distance between any two points along the particle boundary, also known as maximum caliper. The angle (0-180 degrees) of the Feret's diameter is displayed as FeretAngle, as well as the minimum caliper diameter (MinFeret).
- Feret = Feret's diameter of particle (length in pixels)
- FeretX = Coordinate of one end of Feret's diameter.
- FeretY = Coordinate of one end of Feret's diameter.
- FeretAngle = Angle between Feret's diameter and x-axis.
- MinFeret = Minimum Feret's diameter of particle (length in pixels)
Filtering Particles by Size and Circularity
The number of particles returned by analyzeparticles can be reduced by specifying a minimum or maximum area or circularity that a particle must have. These values can be specified as options.minsize, options.maxsize, options.mincircularity, options.maxcircularity, or default values will be used.
Reverse Mask to Measure Bright Particles
The default behavior is to identify particles as connected regions which have intensity above a threshold value. This identifies brighter areas as particles while the rest of the image is considered a darker background. In some images, however, the particles may appear as darker spots on a brighter background. Such particles can be analyzed by setting the input option "reversemask" to "off" instead of its default value "on".
Handling of Holes Within Particles
The default behavior of analyzeparticles, option.includeholes = 'on', is to measure a particle's area or mean pixel value, etc. by including all enclosed pixels. Thus any holes within an enclosing particle do contribute to the particle's area or mean pixel value. This behavior can be changed by specifying the input option.includeholes = 'off', which will mean that non-particle pixels within the surrounding particle boundary are not used in calculating the particle area or mean pixel value, etc.. When option.includeholes = 'off' any "child" particles within such a hole are reported as additional particles and do not contribute to the enclosing particle's area and mean, etc. Thus, includeholes = 'off' can lead to identifying more particles. A set of N concentric circles would count as just one particle if includeholes = 'on' but would yield N particles when includeholes = 'off'.
Handling of Excluded Pixels
Pixels which are flagged as excluded by the dataset object are treated as non-particle pixels.