![]() “Keep members” (keeps the particles that match the query and deletes the rest),.OR = (Class) is true) OR (Class is true) OR (Class is true) OR (Class is true)Ĭlasses which are left empty are ignored. Currently supported are: AND = (Class is true) AND (Class is true) AND (Class is true) AND (Class is true) “Combine” allows to set a logical constrain for the result. operator=> value=0.85 class=-empty- operator=-empty- value=0.0000 combine= output= white title=Subset") Ĭheck “White particles” for white particles on a black background (or leave unchecked for black particles on a white background). run("Classify Particles", "class=Area operator=>= value=200 class=Perim. This can also be recorded as a macro (mind the line breaks). =200 AND Perimeter >= 40 AND Circularity >0.85. The logical operator is one of the following: > The morphological parameters are the columns in the Results Table. Here the user defines up to 4 classes by selecting a morphological parameter, a logical operator and a value for each class. If any of these tests fail, an error message shown with further instructions, otherwise the main dialog will appear: If two names clash (for example: “ Circ.” and “ C-ir*c” are both reduced to “ Circ“, similarly “Area” and “%Area” will clash), then it is not possible to process the query correctly since both variables would have the same name. The plugin deletes all non alphanumeric characters (for instance “ Dist.” becomes “ Dist“. Do the column names in the Result Table clash after removing non-word characters? The column names are converted to macro variable names and they cannot contain invalid characters.The Particles4, Particles8 and Lines8 all output the particle starts by default. If you are using the Particle Analyzer, please check the Record Starts option. The reconstruction uses the particle start coordinates (this is a pixel that is guaranteed to be in the particle) as seed and the original image as the mask. Have the particle Start Coordinates been recorded in the Results Table? As mentioned above, the plugin uses Binary Reconstruction to keep or delete particles (the Binary_Reconstruct plugin is included in the Morphology collection).The Particles4, Particles8 and Particles8_Plus all output the slice number by default. Please check that option even for single images before running the Particle Analyzer. ImageJ v1.35j added the option to output the slice number (Analyze>Set Measurements >Stack position) for the Particle Analyzer. Is the Slice Number recorded in the Results Table? The plugin can process single images or stacks, but it must know to which slice each particle belongs to.Is there an active Results Table? The plugin uses the data stored in the Results Table to classify the particles, so if there is no Table, there is no data to base the classification on.See below an example for dealing with greyscale images. In that case, the image needs to be thresholded before running this plugin. ![]() The Particles4, Particles8 and Lines8 plugins all work on binary images, but the built-in Particle Analyzer can process greyscale images too. Is the current image binary? The plugin works only with (8-bit) binary images because uses Binary Reconstruction to keep/delete particles that match (or do not match) a particular query.The Classify_Particles plugin, at run time, performs 5 tests: The particle Starts (XStart, YStart) must be in the Results Table.The Slice number must be in the Results Table.A valid open Results Table, which holds the data to classify the particles.A binary 8bit image open in ImageJ containing the particles to be classified.ImageJ version 1.35j or later (if you intend to use the data generated by the built-in Particle Analyzer).In brief, the Classify_Particles plugin expects: Note that the macro is re-written with new parameters each time the plguuin is run. The plugin is a front end to generate and run a macro named Particle_Classifier.ijm that will be automatically stored in the macros folder. Those parameters are usually extracted by other plugins (such as the built-in Particle Analyzer, Particles4, Particles8 and Lines8). This ImageJ plugin is part of the morphology plugins collection and can be used to classify binary particles according to morphological parameters in the Results Table.
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