Threshold on interpolated zoomed view

[Maciej Rudzinski]

Hello everyone,

During image review at high magnification I need to apply threshold. At the time I have "interpolate zoomed images" option turned on. The threshold seems to be working off the original non-interpolated image rather than the current view. To work around I re-size the images and then apply the threshold but this is very inconvenient.


I'd appreciate any input or ideas on how to solve this with a macro or any other way.

Regards,

Maciej Rudzinski

[Wayne Rasband]

> Hello everyone,
>
> During image review at high magnification I need to apply threshold. At the time I have "interpolate zoomed images" option turned on. The threshold seems to be working off the original non-interpolated image rather than the current view. To work around I re-size the images and then apply the threshold but this is very inconvenient.

>
> I'd appreciate any input or ideas on how to solve this with a macro or any other way.

You can use a macro something like this:

   run("Capture Image");
   run("8-bit");
   setAutoThreshold("Otsu");
   run("Convert to Mask");

It uses the Plugins>Utilities>Capture Image command to create an interpolated version of the image, then converts it to 8-bits, sets the threshold and applies it. Use setAutoThreshold("Otsu dark") if the image has a dark background. "Otsu" can be replaced with any of the 15 thresholding methods available in ImageJ 1.42 or later.

-wayne

[Michael Schmid]

Hi Maciej,

in my view there is no way to improve this:
If you zoom in, interpolation is only for display, but the image data are
still the original pixels. If you threshold these data, a pixel can be
only red or gray. You can't have a pixel that is partially thresholded.
For all subsequent operations, such as 'Analyze Particles', a pixel can be
inside the thresholded area or outside, nothing in between. There is no
way to have an information like "The upper 1/5 of the pixel are
thresholded". After all, a pixel is by definition the smallest entity in
an image.

So your solution of Adjust Size with interpolation is the only way to get
what you want.

Michael
_______________________________________________________________________

On Sat, December 19, 2009 17:59, Maciej Rudzinski wrote:

> Hello everyone,
>
> During image review at high magnification I need to apply threshold. At
> the time I have "interpolate zoomed images" option turned on. The
> threshold seems to be working off the original non-interpolated image
> rather than the current view. To work around I re-size the images and then
> apply the threshold but this is very inconvenient.
>
>
> I'd appreciate any input or ideas on how to solve this with a macro or any
> other way.
>
> Regards,
>
> Maciej Rudzinski
>

[Maciej Rudzinski]

Wayne,

Many thanks!
I'll follow you suggestion.

Regards,

Maciej

----- Original Message -----
From: "Wayne Rasband" <[hidden email]>
To: [hidden email]
Sent: Saturday, December 19, 2009 8:09:42 PM GMT -08:00 US/Canada Pacific
Subject: Re: Threshold on interpolated zoomed view

> Hello everyone,
>
> During image review at high magnification I need to apply threshold. At the time I have "interpolate zoomed images" option turned on. The threshold seems to be working off the original non-interpolated image rather than the current view. To work around I re-size the images and then apply the threshold but this is very inconvenient.

>
> I'd appreciate any input or ideas on how to solve this with a macro or any other way.

You can use a macro something like this:

run("Capture Image");
run("8-bit");
setAutoThreshold("Otsu");
run("Convert to Mask");

It uses the Plugins>Utilities>Capture Image command to create an interpolated version of the image, then converts it to 8-bits, sets the threshold and applies it. Use setAutoThreshold("Otsu dark") if the image has a dark background. "Otsu" can be replaced with any of the 15 thresholding methods available in ImageJ 1.42 or later.

-wayne

[Maciej Rudzinski]

Michael,

Thank you for your inputs.

Regards,

Maciej R.

----- Original Message -----
From: "Michael Schmid" <[hidden email]>
To: [hidden email]
Sent: Sunday, December 20, 2009 12:30:07 PM GMT -08:00 US/Canada Pacific
Subject: Re: Threshold on interpolated zoomed view

Hi Maciej,

in my view there is no way to improve this:
If you zoom in, interpolation is only for display, but the image data are
still the original pixels. If you threshold these data, a pixel can be
only red or gray. You can't have a pixel that is partially thresholded.
For all subsequent operations, such as 'Analyze Particles', a pixel can be
inside the thresholded area or outside, nothing in between. There is no
way to have an information like "The upper 1/5 of the pixel are
thresholded". After all, a pixel is by definition the smallest entity in
an image.

So your solution of Adjust Size with interpolation is the only way to get
what you want.

Michael
_______________________________________________________________________

On Sat, December 19, 2009 17:59, Maciej Rudzinski wrote:

> Hello everyone,
>
> During image review at high magnification I need to apply threshold. At
> the time I have "interpolate zoomed images" option turned on. The
> threshold seems to be working off the original non-interpolated image
> rather than the current view. To work around I re-size the images and then
> apply the threshold but this is very inconvenient.
>
>
> I'd appreciate any input or ideas on how to solve this with a macro or any
> other way.
>
> Regards,
>
> Maciej Rudzinski
>