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nanosims:lans_extras:watershed_roi_segmentation

Watershed segmentation of ROIs

2017-11-04:

My nanosims image shows a larger 'blob' of relatively high but quite variable ion counts. Could I use some automated image processing tool, such as watershed segmentation, to segment this pattern into several smaller ROIs?

Possible solution

  1. When defining ROIs through the INTERACTIVE ROIs definition tool, select Split ROIs via watershed segmentation through the Action menu. click for full-size
  2. When prompted, decide about the minimum size of ROIs that you want to keep after this segmentation.

Example

  1. In the main LANS GUI specify the ROI definition template, and select ROIs → INTERACTIVE ROIs definition tool from the main LANS menu.
  2. In the tool window, define first the larger ROIs that you will want to divide into smaller ROIs by watershed segmentation.
  3. In the Action menu, select Split ROIs via watershed segmentation. This will split the defined larger ROIs into many ROIs of different sizes. The distribution of these sizes will be displayed in a histogram, as shown below. click for full-size
  4. Using this histogram, decide about the minimum size of ROIs that you want to keep after this segmentation. Enter this minimum size to the dialog window that pops up and click OK.
  5. Based on this information, the segments with size below this threshold will be merged with neighboring ones so that, in the end, no ROI smaller than the given threshold size will be left. You can watch the progress of this merging in the Matlab console. At the end, the updated segmentation together with the histogram of ROI sizes will be again displayed. click for full-size
  6. If you are satisfied with the results, click Yes in the dialog window that pops up. Subsequently, the outlines of the ROIs will be displayed in the window of the ROI definition tool. click for full-size

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nanosims/lans_extras/watershed_roi_segmentation.txt · Last modified: 2017/11/18 05:55 (external edit)

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