Blobs

In DigImage, a "blob" is defined as a connected region of an image falling entirely on one of a specific threshold. Connection may be defined either with or without diagonal connections. This option is able to locate all blobs within a window and evaluate statistics about each blob. These statistics include the area, location of the blob centroid (both area and the centroid of the volume satisfying the intensity threshold), maximum extent, rms extent and x-y correlation. All linear blob measures are given in world units.

Output is to a formatted file. Some of the data is presented in the form of comments (preceded by a # character), while the individual particle data is with one particle per line. A typical file has the following format:

           # Title
           # Threshold: 128; Sign: -1....

           The data for each blob is written by the following statement:
              WRITE(iFile,300)iBlob,nPoints,AverageInt,xwc,ywc,xww,
                              yww,xMin,xMax,yMin,yMax,xws,yws,Correlation

           In this
                   iBlob      An index
                   nPoints    Number of pixels in this blob
                   AverageInt The mean intensity of the blob
                   xwc,ywc    Position of the centroid of the area occupied
                              by the blob
                   xww,yww    Position of the centroid weighted by intensity
                              excess
                   xMin,xMax,yMin,yMax  The bounding rectangle for the blob
                   xws,yws    The rms width and height.
                   Correlation  The correlation coefficient of pixels within
                              blob (i.e. treat like a scatter plot).

           Note that all the x* and y* values are in world units.

Buffer to locate blobs in ?

A list of buffers to be processed may be specified. Any valid DigImage buffer may be used. The first buffer specified will be used during the specification of the window within which the blobs will be located.

Another buffer ? More than one buffer may be processed at one time. A further buffer may be specified by responding yes (<Y>). Once all the buffers required have been entered, an answer of no (<N>) will allow DigImage to continue with the next phase of blob location.

Blobs in Window or whole Screen ?

The blobs may be located either in the entire image (<S>), or a window within each image (<W>).

Window Selection: Region to find blobs in

If the user has decided to locate blobs within a specific window, then the Window Selection submenu will be produced to allow the desired window to be specified. If a blob lies only partly inside the window, then the statistics will be evaluated only on that part within the window. This situation may subsequently be determined by looking at the extremes of the particle and comparing it with the window boundaries. The [H Help] facility within the windows submenu provides details on how to specify the window.

Search over 4 or 8 neighbours ?

This entry specifies the degree of connectivity the pixels within a blob must have. If <4> is specified, then regions connected only along a diagonal will not be included, whereas if <8> is chosen, then they will. The mechanics of determining which pixels lie within a "blob" revolves around searching the four or eight nearest neighbours to find a pixel satisfying the required intensity requirements. This pixel is then mark added to a list of pixels to be searched around during the next phase.

Intensity defining blob ?

This entry specifies the minimum or maximum intensity (depending on the next field) a pixel may have to be included as part of a blob.

Blobs Greater of Less than this value ?

This entry dictates whether the blob is greater (<G>) or less than (<L>) the threshold intensity specified by the previous entry.

Name of formatted output file (.DAT default extension) ?

The name of the formatted file to which the locations and statistics of the various blobs located within each buffer are written. The format of this file is given earlier in this help text. If no file is specified, then a summary only of the data is produced and written to the computers monitor.

New or Append ? If the specified file already exists, replying <N> to this question forces DigImage to start a new file; if <A> is pressed, then the existing contents are preserved and the data produced by the blob statistics is appended. If the file specified does not already exist, then the reply to this option is ignored and a new file is always created.

Title for file ?

The character string specified by this entry is added to the output file as a comment (prefixed by #).

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Stuart Dalziel, last page update: 19 February 1996