AutoThreshold

[Bill Rothman]

The default B&W auto thresholding works pretty good for my images for a
first screening. Where is it's actual method described (in Sankar 2004?)
I'd like to capture the min,max threshold values found in a text file in
the macro I've built which automatically batch processes a few hundred
images. I'd like this text file to pick up the particle analysis totals,
in addition to each result xls file I'm saving.

[Gabriel Landini]

On Thursday 10 December 2009 20:56:10 you wrote:
> The default B&W auto thresholding works pretty good for my images for a
> first screening. Where is it's actual method described (in Sankar 2004?)

Have a look in:
http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold

It is a version of the isodata algorithm of:
Ridler, TW & Calvard, S (1978), "Picture thresholding using an iterative
selection method", IEEE Transactions on Systems, Man and Cybernetics 8:
630-632.

Several implementations of this method exist one is the "default", another is
the isodata.

> I'd like to capture the min,max threshold values found in a text file in
> the macro

There is only 1 value, the threshold value. The "other" value is 0 if the
object is dark or 255 if bright (when using 8bit images). You can print the
threshold value to a log window if you use the plugin from:

http://www.dentistry.bham.ac.uk/landinig/software/auto_threshold.jar

This will create 2 new commands in Image>Adjust>Auto_Threshold and
Auto_Local_Threshold.

You need to check the box "Show threshold values in log window".

There is another advantage in using the plugin in which you can select whether
the extreme histogram bins are ignored or considered in the threshold
computation. The built-in thresholder in IJ uses "ignore black" and "ignore
white" for the default method, but does not ignore those bins for the rest.

The built-in thresholder, however, can threshold 16 and 32 bit images (which
get binned to 256 ranges).
Cheers

G.