Thresholding

[John Bishai]

Hello,
I had a question about the difference between auto threshold and apply threshold. I understand that  
"auto threshold" figures out the ideal max and min values while the apply comand allows one to
manually set the values. However , when I use the same min and max values for "apply" as was
chosen for "auto" I get different values for my analysis. Do both auto and apply convert the images to
binary?  Can anyone explain this?
Note: after I select apply I check all the boxes for Apply LUT.
Thanks.
John

[Justin Murdock-2]

In regards to the facet orientation plugin (or the facet calculation in
SurfCharJ), is the angle of each pixel calculated or can you define a
minimum length/area that will be analyzed for orientation.



Justin

[Robert Dougherty]

Justin,

It's every pixel.  One way to specify a minimum size would be to low-pass
filter the image before running facet orientation.  Try Process/FFT/Bandpass
Filter... and enter the minimum length in the box "Filter Small Structures
Up to."  The limit for large structures should be set to a size that is
larger than any feature you are interested in.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Justin Murdock
> Sent: Monday, October 31, 2005 11:18 AM
> To: [hidden email]
> Subject: Facet orientation
>
> In regards to the facet orientation plugin (or the facet calculation in
> SurfCharJ), is the angle of each pixel calculated or can you define a
> minimum length/area that will be analyzed for orientation.
>
>
>
> Justin

[Justin Murdock-2]

Thanks Bob, this info is very helpful.

Justin

Quoting Robert Dougherty <[hidden email]>:

> Justin,
>
> It's every pixel.  One way to specify a minimum size would be to
> low-pass
> filter the image before running facet orientation.  Try
> Process/FFT/Bandpass
> Filter... and enter the minimum length in the box "Filter Small
> Structures
> Up to."  The limit for large structures should be set to a size that
> is
> larger than any feature you are interested in.
>
> Bob
>
> Robert P. Dougherty, Ph.D.
> President, OptiNav, Inc.
> Phone [phone]
> Fax [phone]
> www.optinav.com
>
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
> Of
> > Justin Murdock
> > Sent: Monday, October 31, 2005 11:18 AM
> > To: [hidden email]
> > Subject: Facet orientation
> >
> > In regards to the facet orientation plugin (or the facet
> calculation in
> > SurfCharJ), is the angle of each pixel calculated or can you define
> a
> > minimum length/area that will be analyzed for orientation.
> >
> >
> >
> > Justin
>
>

Justin Murdock
Kansas State University
Division of Biology
232 Ackert Hall
Manhattan, KS 66506

[Wayne Rasband]

> I had a question about the difference between auto threshold
> and apply threshold. I understand that  "auto threshold"
> figures out the ideal max and min values while the apply
> comand allows one to manually set the values. However , when
> I use the same min and max values for "apply" as was chosen
> for "auto" I get different values for my analysis. Do both
> auto and apply convert the images to binary?  Can anyone
> explain this?

The "Auto" option in Image>Adjust>Threshold figures out optimum lower
and upper threshold values and updates the LUT so that pixels with
values within this range are displayed in red. The pixel values are not
changed. The "Apply" option converts the image to binary, changing the
pixel values.

-wayne
>