Using a set of points as a seeds, the Region Growing application, for each point in the set, determines the points that are nearby and whose intensity is in an appropriate range.
Set the source for the image data by pressing the Image file button to browse for a file or by entering the window number or file name directly in the field next to the Image file button. You can restrict region growing to a subset of the image data; see Input subset for details. Use the point data button or the field next to it to set the file with the points that are to be used as the starting points for the region growing process. This file must be in the old Pick Points format; it could be generated by Pick Points or FindPoints though the latter can also perform region growing on its own.
For the intensity criteria used to determine whether a point should be included in the region, you have two basic choices:
With either, turn on the Valley toggle to also reject points whose intensity is greater than that of the adjacent point which was just added to the region.
To find the regions, you must also specify an output file by entering a file name or window number in the Out file or Mask file field (you can use both fields, but use a different file name for each). In the Out file, points which do not fall into any region have zero intensity, and all the other points will have the same intensity as they had in the input file. In the Mask file, points which do not fall into any region are set to zero and all other points are labeled by the number of the region to which they belong.
Once the input file, points list, threshold, and output file(s) are selected, press doit to determine what the regions are. While the calculation is in progress, the doit button will be labeled interrupt and can be used to halt the calculation.
Once the regions have been found, the Save button can be used to save some summary results for the regions. The old pick points format is used for these results: the first three columns are the x, y, and z location of the seed point; the fourth column is the region number; the fifth column is the sum of the intensity over the region; and the sixth column is the number of points in the region.
Overview | Input subset
Pick Points | Find Points | Priism
The subset of the input that is used for region growing is set by the XY, Z, and T fields and the wavelength toggles at the bottom of the dialog. The subset has a rectangular cross-section in x and y. The first two values in the XY field are the pixel coordinates of the lower lefthand corner of the rectangle; the last two values are the dimensions, in pixels, for the rectangle. If the input file is a window, the rectangle can be selected using the mouse a recipe for doing this is:
The Z field sets the range of z sections included in the subset. A section is included if its index is greater than equal to the first value in the field, if its index is less than or equal to the second value in the field, and if its index minus the first value in the field is evenly divisible by the third value in the field. The T field is interpreted similarly but applies to the time points included in the subset.
Select the wavelengths included in the subset with the toggles at the bottom of the dialog. The ordering of the toggles from left to right reflects the ordering of the wavelengths in the file: when the leftmost toggle is on, the first wavelength in the file is included; otherwise it is not included.
Overview | Input subset