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06/11/2004

General rules for batch particle sizing.

Crop, Flatten, Scale

1)    Crop any size bars and annotations out of the image.  Otherwise they might be blobbed.

2)    Flatten the images and rescale to byte.  The rescaling is not necessary, but makes better thumbnails, faster display, and sometimes smaller files. If all of your image files have the scale bars in the same place, one cropping rectangle might do for the lot.  Here are example process folder commands for crop, flatten and rescale using

The flatten parameter should get rid of the uneven background illumination, but not be so small that particles are also flattened so that they are bright edges holes in the middle.  If they look like donuts, the edges might not be completely continuous, and the boundary will 'leak' into the interior of the particle.

Blob the images

4)    Set these parameters in the blob tool window.

If the images are uniform enough to allow the  use of one threshold setting for all of them, then set the thresholds on a threshold slider: .

5)    Set the blob folder - '+ / b / Set'.  Blob files, which save the outlines for the particles in each image, go here.

6a)   Blob the files using 'Tools / Process folder / Files in folder / Blob'. If the images are not uniform enough to allow use of one threshold setting for all, then blob them individually.

6b)  Threshold slider / ?Windows? / Front image.

The outline information is in the blob folder in a file named <image name>-nn.blob.  If the image is blobbed more than once, nn increases from 00 on up.  These blob files supply information for supsequent processing steps such as 7.

You might want to check what statistics will be saved in the next file using 'Blob buttons / stats / which stats selected?'

7)    Record blob information to a text file.

'Tools / Process folder / Files in folder / Blob stats to file'. This text file can be read by Excel.