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05/13/2008

Stats or Form Factors - definitions

Blob Tool

Statistics  ('Stats' button)

Stats Button 

The functions include:

Selecting statistics (see categories above), listing them, and making new statistics.

Clearing individual statistics (they are chosen by categories) and clearing certain kinds of statistics.  This does not save much calculation time, but it might avoid clutter in your output.

 

Listing measurements for individual objects or blobs.

 

Summarizing the measuremts.

 

Plotting the statistics.

Making a spreadsheet for further examination of the statistics or for exporting them.

 

 

      Parameters such as area and centroid that describe the intensitiy, location and shape of each blob can be selected for each blobbed image.  They are available after blobbing, and can be changed without re-blobbing.

      Summary statistics for all the blobs together are available after blobbing for all of the shape and intensity parameters previously selected. 

Set Stats                     Choose parameters to print.  Defaults to last selection.
List selected stats?         Lists parameters chosen for the Blob Img.
Print table                   Prints text tab-delimited table of blob parameters.
Print sel blob                Select blob by index (other parameters are shown also). Prints parameters for this blob only.
Sorted stat list              Prints sorted list of the selected blob parameter.
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Set Summary Statistics        Choose one or more of :mean :min :max and :variance.
Summary stat titles           Prints titles in a tab delimited row for spreadsheets.
Summary stat values           Prints values in a tab delimited row for spreadsheets.
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Histogram                    
2-D Plot                     .
3-D Plot    Not yet implemented.
Note - when a parameter has more than one value, such as the centroid (x y) which has two, the statistics are reported for each of the values in turn, as if they were distinct parameters.  For the centroid, centroid-1 mean is the mean for all of the X values. 
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Using summary statistics for particles in a number of images:
1  Make a threshold slider window and initialize the minimum area and
touch edge parameters.
      +  '***Buttons*** / Th!' - makes a thresholder slider.
      +  (See above for Threshold Slider menus.)
2  Set parameters in this (*Blob Buttons*) window.
      +  Blob parameters:  'Stats / Set stats',  choose among: area, perimeter, ....  See 'Info / Blob Parameters' for a list of theparameters.
      +  Summary statistics:  'Stats / Set summary statistics', choose among mean, min, ...
      +  If you expect more than 4096 blobs in your image, increase n_blobs to a safe number with the  'Parameters' button.
3     Load an image
            Most common way is with '***Buttons*** / File / Open'
4     Select the thresholds and blob.
      +  In the Threshold Slider, use '?Windows? / Front window' to make the slider work on the image.
      +  Drag the left, center or right parts of the red slider bar to select objects. Objects should be red.
      +  In the Threshold Slider, use 'Thresholds / Blob'. See the green outlines and the blob labels.
5     If this is the first image, print the summary stat titles 'Stats / Summary stat titles'
6     Print the statistics values:  'Stats / Summary stat values'.
7     Close the image, do steps 3-6 for other images.
8     Cut and paste the summary stats into either a spread sheet or text file as desired. The rows are tab delimited, so the titles and values will line up in, say, Excel, even if they do not appear to line up in the Lispix text output window.