usage:advanced_usage

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usage:advanced_usage [2020/06/26 10:56] – [Custom feature extraction] pseudomoanerusage:advanced_usage [2022/09/05 23:05] (current) – pseudomoaner
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 If using the stand-alone version of FAST, functions that can write .mat files from other languages (such as R's [[https://www.rdocumentation.org/packages/R.matlab/versions/3.6.2/topics/writeMat|writeMat]] function) should be used to perform this step. If using the stand-alone version of FAST, functions that can write .mat files from other languages (such as R's [[https://www.rdocumentation.org/packages/R.matlab/versions/3.6.2/topics/writeMat|writeMat]] function) should be used to perform this step.
  
-You will also need to provide FAST with the raw images from your dataset. This can be performed using FIJI in a similar way to the the segmentations, but each file ('Frame_0000.tif' etc.) should be save in a folder named 'Channel_N', where N indicates the index of the channel that image represents. For example, the 5th image of the 2nd channel in your dataset should be saved under 'root/Channel_2/Frame_004.tif'.+You will also need to provide FAST with the raw images from your dataset. This can be performed using FIJI in a similar way to the the segmentations, but each file ('Frame_0000.tif' etc.) should be saved in a folder named 'Channel_N', where N indicates the index of the channel that image represents. For example, the 5th image of the 2nd channel in your dataset should be saved under 'root/Channel_2/Frame_004.tif'.
  
 ==== Custom feature extraction ==== ==== Custom feature extraction ====
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 %   OUTPUTS: %   OUTPUTS:
 %       -feats: Vector of extracted feature values. If inSeg and inChans %       -feats: Vector of extracted feature values. If inSeg and inChans
-%       are empty, should return a vector of zeros of the same size - this+%       are empty, should return a vector of zeros of the same size as  
 +%       the output feature vector if these inputs were not empty - this
 %       is used to initialise storage in the feature extraction engine. %       is used to initialise storage in the feature extraction engine.
 % %
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 %   OUTPUTS: %   OUTPUTS:
 %       -feats: Vector of extracted feature values. If inSeg and inChans %       -feats: Vector of extracted feature values. If inSeg and inChans
-%       are empty, should return a vector of zeros of the same size - this+%       are empty, should return a vector of zeros of the same size as  
 +%       the output feature vector if these inputs were not empty - this
 %       is used to initialise storage in the feature extraction engine. %       is used to initialise storage in the feature extraction engine.
 % %
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   * **Locations** defines the columns in **trackableData** that should be included as separate features. For example, each cell in **trackableData.Centroid** contains an Nx2 matrix of values, with the first column indicating the x-coordinate of the N objects and the second column the y-coordinate. As checking the **Position** box in the tracking module indicates that you wish to include both x and y coordinate data as features, **featureStruct.Centroid.Locations** is set as [1,2].   * **Locations** defines the columns in **trackableData** that should be included as separate features. For example, each cell in **trackableData.Centroid** contains an Nx2 matrix of values, with the first column indicating the x-coordinate of the N objects and the second column the y-coordinate. As checking the **Position** box in the tracking module indicates that you wish to include both x and y coordinate data as features, **featureStruct.Centroid.Locations** is set as [1,2].
   * **StatsType** defines if your feature is circular or linear.   * **StatsType** defines if your feature is circular or linear.
-  * **Range** only needs to be defined if **StatsType** is set as circular, and sets the 'seams' of the wrapped number line. For example, the object orientation **phi** transitions smoothly from -90^o to 90^o; **featureStruct.Orientation.Range** is therefore set as [-90 90].+  * **Range** only needs to be defined if **StatsType** is set as circular, and sets the 'seams' of the wrapped number line. For example, the object orientation **phi** transitions smoothly from -90° to 90°; **featureStruct.Orientation.Range** is therefore set as [-90 90].
  
 === Informing the division detection module === === Informing the division detection module ===
  • usage/advanced_usage.1593165372.txt.gz
  • Last modified: 2020/06/26 10:56
  • by pseudomoaner