OPS>SOFTWARE>DOCUMENTATION>EXPORT ORIENTATION LINES

How to export Orientation Lines (Angle information) to an Excel spreadsheet

  • 1. Manually export using ImageJ functions
  • 2. Automated export using ImageJ/OpenPolScope macro sub plugin (requires OpenPolScope ver. 2.15 or above)
    • Orientation Image scaling convention (where not computed for display by OpenPolScope software):
      8-bit: 0 - 179; 179 pixel value corresponds to 179
      12-bit: 0 - 1790; 1790 pixel value corresponds to 179 (1790/10)
      14-bit: 0-7160; 7160 pixel value corresponds to 179 (7160/40)
      16-bit: 0 - 17900; 17900 pixel value corresponds to 179 (17900/100)

      1. Manually export using ImageJ functions

      Select a roi section or use the full image to plot the Orientation Lines

      Orientation Lines

      In ImageJ select Plugins > Macros > Run...

      Orientation Lines

      This will bring up ImageJ's Macro selector.

      Orientation Lines

      The Orientation Lines will then be imported into the ROI-Manager (column-wise). This is 0-indexed (starts with 0 numbering)

      Orientation Lines

      The ROIs on the image will now show their labels as well.

      Orientation Lines

      The Measure result pops in a new Result table. This is not 0-indexed (starts with 1 numbering)

      Selecting a label in ROI-Manager will select the selected plot line eg. 0002-0011-0155. This corresponds to number 12 in the Results table.

      Orientation Lines

      The Results table shows the Angle of the lines and its corresponding length. If the lines are plotted using the option 'lengthPropRatio' this would correspond to Anisotropy or Retardance as the case may be. Please note the line is scaled based on x/y interval. Using the Result table's File menu one can export the data into an excel spreadsheet.

      Orientation Lines
      One can also Save/Open the ROIs for later referencing to Results using 'More' button on the ROI-Manager.

      2. Automated export using ImageJ/OpenPolScope macro sub plugin (requires OpenPolScope ver. 2.15 or above)

      Requires ImagejMacro sub plugin.


      Select a roi section or use the full image to plot the Orientation Lines

      Orientation Lines

      In the Processing tab select ImagejMacro-Pre plugin and select '...' button for more options

      Orientation Lines

      In ImagejMacro-Pre using the 'Select Macro' button select 'Export_Orientation_Lines.ijm' macro and set options as below

      Orientation Lines

      Selecting 'Edit' will open the editable interface. Here one can set a path to save otherwise one can save the results at the end

      Orientation Lines

      If the data has been already processed one can disable re-processing by selecting 'Dont Process' under Options in the Pol-Analyzer interface. Also, Parallelize Processing needs to be disabled for this operation.

      Orientation Lines

      Selecting the Process button will start the export process. If there are multiple time and/or z-slices the results are appended and will require to be arranged accordingly.

      Orientation Lines

      Orientation Lines

      Please read the Manual export section to understand the ROI/Result relation explained by an example

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Last Page Update on September 12 2013 16:01