Evriscript and Analyzeparticles: Difference between pages

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===Purpose===
===Purpose===


EVRISCRIPT objects allow calling various PLS_Toolbox operations in an
ANALYZEPARTCLES Identify particles (blobs, connected regions), and their properties, in an image dataset.
object-oriented way. A script can contain one or more steps, each of
 
which is a separate object with its own inputs and outputs. Each step is
===Synopsis===
defined by a keyword which represents the type of step (known as a
 
module) to perform.
: [x model] = analyzeparticles(x, options);                           
: [x model] = analyzeparticles(x);                                   
: [x model] = analyzeparticles(x, model);


===Description===
===Description===
====Creating a script====
Call evriscript with parameters indicating the sequence of steps to
perform, each step indicated by its keyword. The list of available
step keywords is given by the command:  evriscript_module('showall')
Example, myscript = evriscript( 'pls', 'crossval', 'choosecomp', 'pls');
  myscript = evriscript(keyword,keyword,...);  % create a script with two or more steps


'myscript' is an evriscript object. The script steps are evriscript_step
The particle analysis functionality is used to automatically identify particle-like areas in an image and to 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”.
objects which can be accessed by indexing, 'myscript(1)', for example.
 
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====
 
* '''model''' = a standard model structure model with the following fields (see MODELSTRUCT):
** '''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,
* '''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?
* '''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),
* '''particleferet''': [ {'off'} | 'on' ] measure Feret diameters of particle (pixels).
 
===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 pixel  having values below or above the threshold value are assigned value 0 or 1. 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.
 
*'''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 set of particles returned by analyzeparticles can be reduced by specifying the 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 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.. Any "child" particles within such a hole do contribute to the enclosing particle's area and mean, etc. in all cases.
 
====Handling of excluded pixels====
Pixels which are flagged as excluded by the dataset object are treated as non-particle pixels.
 
===See Also===


The individual steps' properties are then configured. Most steps have
[[analysis]], [[particlegui]]
more than one 'step_mode', for example 'calibrate', 'apply' or 'test'.
You can see which step_modes are avaialable for a step by entering
myscript(1).step_module.
This also shows the required and optional properties associated with the
step for each step_mode. The 'calibrate' step_mode lists required
properties as: 'x', 'y', and 'ncomp'.

Revision as of 00:51, 11 February 2011

Purpose

ANALYZEPARTCLES Identify particles (blobs, connected regions), and their properties, in an image dataset.

Synopsis

[x model] = analyzeparticles(x, options);
[x model] = analyzeparticles(x);
[x model] = analyzeparticles(x, model);

Description

The particle analysis functionality is used to automatically identify particle-like areas in an image and to 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

  • model = a standard model structure model with the following fields (see MODELSTRUCT):
    • 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,
  • 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?
  • 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),
  • particleferet: [ {'off'} | 'on' ] measure Feret diameters of particle (pixels).

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 pixel having values below or above the threshold value are assigned value 0 or 1. 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.
  • 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 set of particles returned by analyzeparticles can be reduced by specifying the 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 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.. Any "child" particles within such a hole do contribute to the enclosing particle's area and mean, etc. in all cases.

Handling of excluded pixels

Pixels which are flagged as excluded by the dataset object are treated as non-particle pixels.

See Also

analysis, particlegui

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