This macro helps to visually identify features in images according to their shape properties. The interactive plots enable to hover over the plot surface or retreiving the plot list to determine potential exclusion parameters which consecutively can be used with the "Advanced Particle Analyzer". To finally abort the macro when interactive plots is active "Esc" needs to be pressed. Since version 0.6, when "interactive plots" is enabled, the user can simply click on one of the slices in the color coded output stack to receive a plot of the respective size sorted shape descriptor. The highest descriptor values can also be displayd as an orientation. A calibration bar (LUT can be selected in the setup) enables easier overview and interpretation. The respective shape descriptors are indicated in each slice. Purpose: Shape descriptors of the particles in an 8-bit binary image will be color coded (smallest to biggest values) and are shown in a stack containing the original image in the first slice and the "shape descriptor maps" in the consecutive ones. How to: only works on individual 8-bit binary images. Russ, The Image Processing Handbook, 2010, 6th Edition). This underestimation is proportionate to the particle size. This is recommended as a correction for the bias when measuring features in a field of view because bigger particles are more likely to touch the edges of the field of view and thus their area is are underestimated. With "ImgWidth" and "ImgHeight" as the size of the analyzed image and "BBWidth" and "BBHeight" as the bounding box dimensions of each particle. Purpose: The macro eliminates all particles in a binary image which touch the edges, then counts the remaining particles and corrects for the counting and the mean area bias due to the edge intersection using the following formula:Ĭount correction factor = (ImgWidth * ImgHeight) / ((ImgWidth-BBWidth) * (ImgHeight-BBHeight)) It is already sufficient to cut a zero after the comma without changing the actual parameter value to make the recorder recognize that the entry should be recorded!) Older Macros should still run, while the keyword "pixel" needs to be shifted before the definition of the area parameter.įorm: plugin (recordable, uses smart recording -> records only fields which have been changed by the user while recording. The checkbox "output in pixels" gives the option to separately choose if the results table should be in specific units or pixels (depending on the image calibration). function and uses pixels instead of calibrated units to limit the analysis with the respective parameters. The checkbox "Pixel units" is equivalent to the checkbox with the same label in the standard IJ Analyze Particels. The new version from 11th February 2018 (included from BioVoxxel_Plugins-2.0.1) on contains 2 checkboxes which enable the choice between pixel and calibrated units in images which are spatially calibrated. Shape descriptors which are not available under "Analyze Particles." in IJ or Fiji so far are:Įxtent = / Ĭompactness = / įeret's AR = / Ĭoefficient of variance (CoV) = / Tipp: use the "Shape Descriptor Maps" macro to figure out possible cut-off value combinations for your analysis which you can then use in the Extended Particle Analyzer. This corrects the particle count for edge touching particles. The option "Keep borders (correction)" eliminates particles from 2 edges and keeps particles touching the two borders of choice. "Redirect" redirects the analysis to a grayscale image which enables to analyze skewness, kurtosis as well as the new measure coefficient of variance (cov). You can use integers as well as numbers containing decimal places. How to: Key in minimal and maximal exclusion values connected with a hyphen. The output types are the same as for the Analyze › Analyze Particles.Įxample: If you want to extract/analyze only particles with a certain Feret's Angle or exclude elongated structures using the aspect ratio (AR) or circilarity you can specify so in the initial dialog box. Thus, setting minimal and maximal exclusion ranges of different parameters enables to extract particles from a binary image. It enables the user to further restrict the analysis on particles according to many more parameter spezifications of shape descriptors and angle orientations. Purpose: The "Extended Particle Analyzer" is based on the ImageJ "Analyze Particles." command.
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