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plugin:utilities:tapas_tutorial_:segmentation:start [2019/01/23 05:26]
tboudier
plugin:utilities:tapas_tutorial_:segmentation:start [2019/01/23 05:45] (current)
tboudier [Hysteresis thresholding]
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 ===== Hysteresis thresholding ===== ===== Hysteresis thresholding =====
 The algorithm Hysteresis Thresholding is implemented in the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]] and is described [[plugin:segmentation:3d_spots_segmentation:start|here]].  The algorithm Hysteresis Thresholding is implemented in the [[plugin:stacks:3d_ij_suite:start|3D ImageJ Suite]] and is described [[plugin:segmentation:3d_spots_segmentation:start|here]]. 
-Basically +Basically two thresholds are defined, a high and a low threshold. Objects are first thresholded with the low threshold, only objects having a value higher than the high threshold value are retained, other objects are discarded.  
 + 
 +In our example we define the two thresholds 65 and 128 as explained in the above section about basic thresholding. We can build an image with three values, 0 (displayed in black) for pixels with value below the low threshold, 128 (displayed in gray) for pixels with value above low threshold but below high threshold, and 255 (displayed in white) for pixels with value above high threshold. 
 + 
 +{{:plugin:stacks:3d_ij_suite:dot_blot-inv.png_multi.png?256|}} 
 + 
 +Only gray objects containing white pixel will be retained, other will be discarded. We then obtain the following binary image containing only retained objects.  
 + 
 +{{:plugin:stacks:3d_ij_suite:hyst_dot_blot-inv65-128-Bin.png?256|}} 
 + 
 +The module **hysteresis** will implement the hysteresis thresholding. The low and high thresholds are specified in //minValue// and //maxValue// (there are no default values). 
  
 <code> <code>
-// Iterative thresholding +// hysteresis thresholding 
-// specify minimum and maximum volume +// you need to specify low and high threshold values 
-// and noise level (default 0) +process:hysteresis 
-process:IT  +minValue:65 
-minVolume:10 +maxValue:128 
-</code>+</code> 
  
-In our exampleif we set a minimum volume of 10 we get a lot of noise.+This module can also directly label the image//i.e.// detect and segment the different objects in the image.
  
-{{:plugin:stacks:3d_ij_suite:dot_blot-inv-itmin10.png?256|}}+{{:plugin:stacks:3d_ij_suite:hyst_dot_blot-inv65-128.png?256|}}
  
-A minimum value of 200 allows us to detect all the dots without any background noise objects+You need simply to set the parameter //labeling// to //yes// (the value is //no// by default). 
 +<code> 
 +// hysteresis thresholding 
 +// you need to specify low and high threshold values 
 +// you can label the image directly by setting the parameter labeling to yes 
 +process:hysteresis 
 +minValue:65 
 +maxValue:128 
 +labeling:yes 
 +</code>
  
-{{:plugin:stacks:3d_ij_suite:dot_blot-inv-itmin200.png?256|}} 
  
plugin/utilities/tapas_tutorial_/segmentation/start.txt · Last modified: 2019/01/23 05:45 by tboudier
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