Size distribution example

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04/22/2005

Example

Particle diameter distribution using gray level images.

1) Load image.
a) Set write and blob directories from temp if desired.
2) Measure scale bar.
a) Zoom image, turn drag on, move to see large scale bar.
If you have lost the scale bar, make a navigator: Navigator / Make
b) TOOLS / Profiles / Image!, Line on!, (use East direction)
Drag circles to ends of scale bar and read length at top.
If 'Drag is ON', turn it off to drag the small green circles.
3) Crop annotations out of image
a) Zoom down to 1 again, or to where entire image is visible.
b) 'Select / Draw rectangle',
c) Correct rectangle to exact positions, if desired. For example it is difficult to mouse the upper left corner exactly. Use 'Select / set by typing / x1 y1 x2 y2' to make the origin 0 0.
c) Crop image using 'Select / Crop to rectangle'. (This makes a copy of your image.)
4) Examine image for dim particles.
a) CLUT / gamma slider , CLUT / contrast slider, or CLUT / thermal slider
5) Flatten image if necessary.
a) Filter / Variable. Set kernel radius to, say, 10 pixels.
b) 2-D filter / Flatten
6) Threshold the image with a threshold slider. Make all particles RED.
a) CLUT / threshold slider, if a threshold slider is not already there.
7) Blob the image
a) TOOLS / blob
b) Set minimum area and whether or not to include blobs that touch the edge of the field of view. min area!, edge?
c) Blob the image: Blob / BLOB
d) Select statistics if desired. 'stats / set stats'.
e) To examine the blob outlines without the labels,
i) Zoom the image if desired.
ii) g! or R! to get rid of whatever drawing is there
iii) P! to show the perimeters. L! to show the labels, 'Draw / Outlines ' for perimeters all in green.
f) To save the image with the outlines, do a print screen: <control>PrintScreen (on the keyboard, not in Lispix), or <alt>PrintScreen. This puts the image of your entire desktop into the clipboard, as if you somehow had pasted it. then in Photoshop:
1) 'File / new', and click OK - the default image size is what is in the clipboard.
2) 'File / Paste' - see image. Crop if desired.
8) Save blobbed outlines to file.
'Blob / save to file'.
To save stats for individual file:
1) 'Stats / table'. See new window with stuff in it.
2) Select window, cut and paste to text or Excel file.

To save stats for all image files in a folder:

1) Blob and save outlines for all files individually. Unless the images are very uniform, each will require special treatment - different threshold, different degree of flattening, etc.
2) Make sure the stats in the BLOB window are what you want.
'stats / set stats'
3) 'TOOLS / process folder / Files in folder / Blob stats to file'
Will write a file to the write directory as <date>-stats.txt with the file name, blob index, and the statistics in separate collumns, for one image after another.