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Editing JSON Parameters

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Alex Perez edited this page Aug 10, 2016 · 5 revisions

This page describes, in depth, how to employ custom settings to the morphome analysis pipeline by creating a custom JSON file in a format recognized by morphome.

The custom JSON file must be in the same format as the defaults.json file contained within the morphome package at: morphome/json/defaults.json. Therefore, it is typically good practice to just copy this file to another location and edit the copy.

Links for quick navigation:

Overview of the JSON File Structure

{
    "mitochondrion": {

        "surface_red": 0,
        "surface_green": 1,
        "surface_blue": 0,
        "surface_triangle_multiplier": 1,
        "surface_smooth_iterations": 10, 
        "surface_smooth_lambda": 0.6,

        "skeleton_width": 3,
        "skeleton_smooth_coefficient1": 0.7,
        "skeleton_smooth_coefficient2": 0.2,
        "skeleton_smooth_iterations": 10, 

        "node_red": 1,
        "node_green": 0,
        "node_blue": 0,  

        "write_animation": 0
    },
 ...
}

Surface Parameters

  • surface_red - Red value of the color of the surface displayed, ranging from 0 to 1. NOTE: These and all other color values are only relevant if write_animation is set to 1 for the given organelle.
  • surface_green - Green value of the color of the surface displayed, ranging from 0 to 1.
  • surface_blue - Blue value of the color of the surface displayed, ranging from 0 to 1.
  • surface_triangle_multiplier - Controls the number of triangles contained in the remeshed surface. This changes the third entry under the 'Desired Size' section of the 'Remesh Surface' module, circled in red in the figure below. The value entered here will serve as a multiplier to the total number of triangles in the surface. For example, a value of 1 will use 100% of the input number of triangles, a value of 0.5 will use 50% of the input number of triangles, and a value of 2 will use 200% of the input number of triangles.

  • surface_smooth_iterations - The number of smoothing iterations to use. The greater the number of iterations supplied here, the smoother the surface will be. This value changes the 'iterations' value of the 'Smooth Surface' module, as shown in the figure below.
  • surface_smooth_lambda - The lambda value to use during smoothing. This value must range from 0 to 1, and the greater this value, the smoother the surface will be. However, note that values that are too large can over smooth the surface or create weird artifacts. Values in the range of 0.5-0.8 tend to be most useful. This value changes the 'lambda' value of the 'Smooth Surface' module, as shown in the figure below.

Skeleton Parameters

  • skeleton_width - Width of the skeleton when displayed. NOTE:This value is only relevant if write_animation is set to 1 for the given organelle.
  • skeleton_smooth_coefficient1 - Changes the 'smooth' value under 'Coefficients' within the 'Smooth Tree' module. This value affects how much the raw skeleton is smoothed, and must range from 0 to 1. Larger values will smooth the tree more. See the figure below.
  • skeleton_smooth_coefficient2 - Changes the 'attach to the data' value under 'Coefficients' within the 'Smooth Tree' module. This value affects how much the raw skeleton is smoothed. Larger values will smooth the tree more. See the figure below.
  • skeleton_smooth_iterations - Changes the number of smoothing iterations to be performed. Larger values will smooth the skeleton more. This value changes the 'Number of Iterations' parameter of the 'Smooth Tree' module, as shown in the figure below.

  • node_red - Red value of skeleton nodes, ranging from 0 to 1.
  • node_green - Green value of skeleton nodes, ranging from 0 to 1.
  • node_blue - Blue value of skeleton nodes, ranging from 0 to 1.

Animation Parameters

  • write_animation - When set to 1, a series of 18 TIF images of the object will be written to disk. The TIF images correspond to a 360 degree rotation about the center of the object, with each image corresponding to an incremental 20 degree rotation. When write_animation is set, the Amira GUI will be launched, as this is necessary for writing images and animations. When write animation is not set (i.e. equal to zero), Amira will be launched in -no_gui mode, such that all computations are performed without the GUI.
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