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Threshold only selection - not the full image

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rrmarino

Threshold only selection - not the full image

Hello Great Community!

I need just to threshold a particular selection, not the whole image. Is it possible?

Best Regards,

Rodrigo

PUC-RIO

bwl224

Re: Threshold only selection - not the full image

Dear Rodrigo,

You can use the ROI manager to draw an ROI, and then select that ROI, and
adjust the threshold. You can get results using the "measure" option on
ROI manager.

Best,
Ben

On Wed, Mar 21, 2012 at 6:44 PM, rrmarino <[hidden email]> wrote:

> Hello Great Community!
>
> I need just to threshold a particular selection, not the whole image. Is it
> possible?
>
>
> Best Regards,
>
> Rodrigo
>
> PUC-RIO
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/Threshold-only-selection-not-the-full-image-tp4642650p4642650.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

--
Benjamin Winthrop Little

rrmarino

Re: Threshold only selection - not the full image

Ben,

Thank you very much for answering my question.

I don't know if I am doing something wrong but even after selecting the
ROI, thresholding (using IMAGE - ADJUST - THRESHOLD) still works on the
whole image and not only on the selected ROI I want.

My imageJ is 1.46C

Best Regards,

Rodrigo

On Wed, Mar 21, 2012 at 7:47 PM, Benjamin Little <
[hidden email]> wrote:

> Dear Rodrigo,
>
> You can use the ROI manager to draw an ROI, and then select that ROI, and
> adjust the threshold. You can get results using the "measure" option on
> ROI manager.
>
> Best,
> Ben
>
> On Wed, Mar 21, 2012 at 6:44 PM, rrmarino <[hidden email]> wrote:
>
> > Hello Great Community!
> >
> > I need just to threshold a particular selection, not the whole image. Is
> it
> > possible?
> >
> >
> > Best Regards,
> >
> > Rodrigo
> >
> > PUC-RIO
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.n6.nabble.com/Threshold-only-selection-not-the-full-image-tp4642650p4642650.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
>
>
>
> --
> Benjamin Winthrop Little
>

David Webster

Re: Threshold only selection - not the full image

If you don't need the thresholded ROI to be embedded in the original image,
then do and Image/Duplicate after defining the ROI and threshold the
resulting ROI copy.

David Webster

On Wed, Mar 21, 2012 at 4:46 PM, Rodrigo Marino <[hidden email]> wrote:

> Ben,
>
> Thank you very much for answering my question.
>
> I don't know if I am doing something wrong but even after selecting the
> ROI, thresholding (using IMAGE - ADJUST - THRESHOLD) still works on the
> whole image and not only on the selected ROI I want.
>
> My imageJ is 1.46C
>
> Best Regards,
>
> Rodrigo
>
>
> On Wed, Mar 21, 2012 at 7:47 PM, Benjamin Little <
> [hidden email]> wrote:
>
> > Dear Rodrigo,
> >
> > You can use the ROI manager to draw an ROI, and then select that ROI, and
> > adjust the threshold. You can get results using the "measure" option on
> > ROI manager.
> >
> > Best,
> > Ben
> >
> > On Wed, Mar 21, 2012 at 6:44 PM, rrmarino <[hidden email]> wrote:
> >
> > > Hello Great Community!
> > >
> > > I need just to threshold a particular selection, not the whole image.
> Is
> > it
> > > possible?
> > >
> > >
> > > Best Regards,
> > >
> > > Rodrigo
> > >
> > > PUC-RIO
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://imagej.1557.n6.nabble.com/Threshold-only-selection-not-the-full-image-tp4642650p4642650.html
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> >
> >
> >
> > --
> > Benjamin Winthrop Little
> >
>

rrmarino

Re: Threshold only selection - not the full image

David,

Thank you very much for your attention.

That is exactly what I am already doing, but since it is a CIRCULAR
selection, when it is duplicated the square that fits that selection is
also being duplicated. (Images as far as I know in ImageJ can't be circular)

Any clue mate?

Thanks ,

Rodrigo

On Thu, Mar 22, 2012 at 1:08 AM, David Webster <[hidden email]>wrote:

> If you don't need the thresholded ROI to be embedded in the original image,
> then do and Image/Duplicate after defining the ROI and threshold the
> resulting ROI copy.
>
> David Webster
>
> On Wed, Mar 21, 2012 at 4:46 PM, Rodrigo Marino <[hidden email]>
> wrote:
>
> > Ben,
> >
> > Thank you very much for answering my question.
> >
> > I don't know if I am doing something wrong but even after selecting the
> > ROI, thresholding (using IMAGE - ADJUST - THRESHOLD) still works on the
> > whole image and not only on the selected ROI I want.
> >
> > My imageJ is 1.46C
> >
> > Best Regards,
> >
> > Rodrigo
> >
> >
> > On Wed, Mar 21, 2012 at 7:47 PM, Benjamin Little <
> > [hidden email]> wrote:
> >
> > > Dear Rodrigo,
> > >
> > > You can use the ROI manager to draw an ROI, and then select that ROI,
> and
> > > adjust the threshold. You can get results using the "measure" option
> on
> > > ROI manager.
> > >
> > > Best,
> > > Ben
> > >
> > > On Wed, Mar 21, 2012 at 6:44 PM, rrmarino <[hidden email]> wrote:
> > >
> > > > Hello Great Community!
> > > >
> > > > I need just to threshold a particular selection, not the whole image.
> > Is
> > > it
> > > > possible?
> > > >
> > > >
> > > > Best Regards,
> > > >
> > > > Rodrigo
> > > >
> > > > PUC-RIO
> > > >
> > > > --
> > > > View this message in context:
> > > >
> > >
> >
> http://imagej.1557.n6.nabble.com/Threshold-only-selection-not-the-full-image-tp4642650p4642650.html
> > > > Sent from the ImageJ mailing list archive at Nabble.com.
> > > >
> > >
> > >
> > >
> > > --
> > > Benjamin Winthrop Little
> > >
> >
>

parfait evouna

Re: Threshold only selection - not the full image

Dear Rodrigo, you can also do
Selection
Duplicate
Clear outside
And then threshold
Best regard
Parfait Evouna

Envoyé de mon iPhone

Le 22 mars 2012 à 06:32, "Rodrigo Marino" <[hidden email]> a écrit :

> David,
>
> Thank you very much for your attention.
>
> That is exactly what I am already doing, but since it is a CIRCULAR
> selection, when it is duplicated the square that fits that selection is
> also being duplicated. (Images as far as I know in ImageJ can't be circular)
>
> Any clue mate?
>
> Thanks ,
>
> Rodrigo
>
> On Thu, Mar 22, 2012 at 1:08 AM, David Webster <[hidden email]>wrote:
>
>> If you don't need the thresholded ROI to be embedded in the original image,
>> then do and Image/Duplicate after defining the ROI and threshold the
>> resulting ROI copy.
>>
>> David Webster
>>
>> On Wed, Mar 21, 2012 at 4:46 PM, Rodrigo Marino <[hidden email]>
>> wrote:
>>
>>> Ben,
>>>
>>> Thank you very much for answering my question.
>>>
>>> I don't know if I am doing something wrong but even after selecting the
>>> ROI, thresholding (using IMAGE - ADJUST - THRESHOLD) still works on the
>>> whole image and not only on the selected ROI I want.
>>>
>>> My imageJ is 1.46C
>>>
>>> Best Regards,
>>>
>>> Rodrigo
>>>
>>>
>>> On Wed, Mar 21, 2012 at 7:47 PM, Benjamin Little <
>>> [hidden email]> wrote:
>>>
>>>> Dear Rodrigo,
>>>>
>>>> You can use the ROI manager to draw an ROI, and then select that ROI,
>> and
>>>> adjust the threshold. You can get results using the "measure" option
>> on
>>>> ROI manager.
>>>>
>>>> Best,
>>>> Ben
>>>>
>>>> On Wed, Mar 21, 2012 at 6:44 PM, rrmarino <[hidden email]> wrote:
>>>>
>>>>> Hello Great Community!
>>>>>
>>>>> I need just to threshold a particular selection, not the whole image.
>>> Is
>>>> it
>>>>> possible?
>>>>>
>>>>>
>>>>> Best Regards,
>>>>>
>>>>> Rodrigo
>>>>>
>>>>> PUC-RIO
>>>>>
>>>>> --
>>>>> View this message in context:
>>>>>
>>>>
>>>
>> http://imagej.1557.n6.nabble.com/Threshold-only-selection-not-the-full-image-tp4642650p4642650.html
>>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Benjamin Winthrop Little
>>>>
>>>
>>

Krs5

Re: Threshold only selection - not the full image

Dear Rodrigo,

Another option would be to threshold your image, make your ROI, run Analyse Particles. This will analyse only the particles within the ROI.

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
College of Medicine, Biological Sciences and Psychology
University of Leicester

http://www.le.ac.uk/biochem/microscopy/home.html

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of parfait evouna
Sent: 22 March 2012 06:50
To: [hidden email]
Subject: Re: Threshold only selection - not the full image

Dear Rodrigo, you can also do
Selection
Duplicate
Clear outside
And then threshold
Best regard
Parfait Evouna

Envoyé de mon iPhone

Le 22 mars 2012 à 06:32, "Rodrigo Marino" <[hidden email]> a écrit :

rrmarino

Re: Threshold only selection - not the full image

Dear Straatman and Evouna

Thank you for collaborating with the thread.

Unfortunately that still doesn't solve my problem. I want the threshold
algorithm to look only at the pixels inside the selection, because I am
doing a performance study on different automatic threshold algorithms.

The outside pixels, regardless if I perform a "Clear Outside", are still
influencing on the threshold process, which I am trying to avoid as much as
possible.

Thank you for keep reading this post.

Rodrigo Marino
PUC-RIO, Brazil

On Thu, Mar 22, 2012 at 5:35 AM, Straatman, Kees R. (Dr.) <
[hidden email]> wrote:

> Dear Rodrigo,
>
> Another option would be to threshold your image, make your ROI, run
> Analyse Particles. This will analyse only the particles within the ROI.
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> College of Medicine, Biological Sciences and Psychology
> University of Leicester
>
> http://www.le.ac.uk/biochem/microscopy/home.html
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> parfait evouna
> Sent: 22 March 2012 06:50
> To: [hidden email]
> Subject: Re: Threshold only selection - not the full image
>
> Dear Rodrigo, you can also do
> Selection
> Duplicate
> Clear outside
> And then threshold
> Best regard
> Parfait Evouna
>
>
>
> Envoyé de mon iPhone
>
> Le 22 mars 2012 à 06:32, "Rodrigo Marino" <[hidden email]> a écrit :
>
> > David,
> >
> > Thank you very much for your attention.
> >
> > That is exactly what I am already doing, but since it is a CIRCULAR
> > selection, when it is duplicated the square that fits that selection is
> > also being duplicated. (Images as far as I know in ImageJ can't be
> circular)
> >
> > Any clue mate?
> >
> > Thanks ,
> >
> > Rodrigo
> >
> > On Thu, Mar 22, 2012 at 1:08 AM, David Webster <[hidden email]
> >wrote:
> >
> >> If you don't need the thresholded ROI to be embedded in the original
> image,
> >> then do and Image/Duplicate after defining the ROI and threshold the
> >> resulting ROI copy.
> >>
> >> David Webster
> >>
> >> On Wed, Mar 21, 2012 at 4:46 PM, Rodrigo Marino <[hidden email]>
> >> wrote:
> >>
> >>> Ben,
> >>>
> >>> Thank you very much for answering my question.
> >>>
> >>> I don't know if I am doing something wrong but even after selecting the
> >>> ROI, thresholding (using IMAGE - ADJUST - THRESHOLD) still works on the
> >>> whole image and not only on the selected ROI I want.
> >>>
> >>> My imageJ is 1.46C
> >>>
> >>> Best Regards,
> >>>
> >>> Rodrigo
> >>>
> >>>
> >>> On Wed, Mar 21, 2012 at 7:47 PM, Benjamin Little <
> >>> [hidden email]> wrote:
> >>>
> >>>> Dear Rodrigo,
> >>>>
> >>>> You can use the ROI manager to draw an ROI, and then select that ROI,
> >> and
> >>>> adjust the threshold. You can get results using the "measure" option
> >> on
> >>>> ROI manager.
> >>>>
> >>>> Best,
> >>>> Ben
> >>>>
> >>>> On Wed, Mar 21, 2012 at 6:44 PM, rrmarino <[hidden email]> wrote:
> >>>>
> >>>>> Hello Great Community!
> >>>>>
> >>>>> I need just to threshold a particular selection, not the whole image.
> >>> Is
> >>>> it
> >>>>> possible?
> >>>>>
> >>>>>
> >>>>> Best Regards,
> >>>>>
> >>>>> Rodrigo
> >>>>>
> >>>>> PUC-RIO
> >>>>>
> >>>>> --
> >>>>> View this message in context:
> >>>>>
> >>>>
> >>>
> >>
> http://imagej.1557.n6.nabble.com/Threshold-only-selection-not-the-full-image-tp4642650p4642650.html
> >>>>> Sent from the ImageJ mailing list archive at Nabble.com.
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Benjamin Winthrop Little
> >>>>
> >>>
> >>
>

Theresa Swayne

Re: Threshold only selection - not the full image

Dear Rodrigo,

Experimenting with the "Blobs" sample image, I do get different auto thresholds depending on where I draw the ROI. For example, compare an ROI completely on a blob vs. an ROI including blobs and background. The histogram in the threshold window also reflects the ROI, not the whole image.

So it looks to me like the ROI does determine the pixels considered in auto-thresholding.

Hope this helps.
Theresa

On Mar 22, 2012, at 12:38 PM, Rodrigo Marino wrote:

> Unfortunately that still doesn't solve my problem. I want the threshold
> algorithm to look only at the pixels inside the selection, because I am
> doing a performance study on different automatic threshold algorithms.
>

------------------------------------
Theresa C. Swayne, Ph.D.
Manager, Confocal and Specialized Microscopy Shared Resource
Herbert Irving Comprehensive Cancer Center, Columbia University
1130 Saint Nicholas Ave, 222A
New York, NY 10032

212-851-4613

[hidden email]
http://hiccc.columbia.edu/research/sharedresources/confocal

rrmarino

Re: Threshold only selection - not the full image

Theresa,

Thank you for your advise.

Which version of ImageJ are you using? I am using 1.46c. The histogram
definItely reflects only the selection's pixels but the threshold is still
considering the whole image (I have tried both adding or not the selection
to the ROI manager) . I am accessing it through IMAGE-ADJUST-THRESHOLD.

Maybe there is a setting somewhere that could be activated for you but not
for me.

Best Regards,

Rodrigo Marino

On Thu, Mar 22, 2012 at 1:56 PM, Theresa Swayne <[hidden email]> wrote:

>
> Dear Rodrigo,
>
> Experimenting with the "Blobs" sample image, I do get different auto
> thresholds depending on where I draw the ROI. For example, compare an ROI
> completely on a blob vs. an ROI including blobs and background. The
> histogram in the threshold window also reflects the ROI, not the whole
> image.
>
> So it looks to me like the ROI does determine the pixels considered in
> auto-thresholding.
>
> Hope this helps.
> Theresa
>
> On Mar 22, 2012, at 12:38 PM, Rodrigo Marino wrote:
>
> Unfortunately that still doesn't solve my problem. I want the threshold
> algorithm to look only at the pixels inside the selection, because I am
> doing a performance study on different automatic threshold algorithms.
>
>
> ------------------------------------
> Theresa C. Swayne, Ph.D.
> Manager, Confocal and Specialized Microscopy Shared Resource
> Herbert Irving Comprehensive Cancer Center, Columbia University
> 1130 Saint Nicholas Ave, 222A
> New York, NY 10032
>
> 212-851-4613
>
> *[hidden email]*** <[hidden email]>
> http://hiccc.columbia.edu/research/sharedresources/confocal
>
>

bwl224

Re: Threshold only selection - not the full image

Are the results you are getting using "Measure" reflective of the thresholding within the ROI? Make sure to "set measurements" and include area. See if this changes when you change the size of the ROI. Although the entire image is affected when you adjust the thresholding, calculated results should reflect only the selected ROI
Sent via BlackBerry by AT&T

-----Original Message-----
From: Rodrigo Marino <[hidden email]>
Sender: ImageJ Interest Group <[hidden email]>
Date: Thu, 22 Mar 2012 14:06:59
To: <[hidden email]>
Reply-To: ImageJ Interest Group <[hidden email]>
Subject: Re: Threshold only selection - not the full image

Theresa,

Thank you for your advise.

Which version of ImageJ are you using? I am using 1.46c. The histogram
definItely reflects only the selection's pixels but the threshold is still
considering the whole image (I have tried both adding or not the selection
to the ROI manager) . I am accessing it through IMAGE-ADJUST-THRESHOLD.

Maybe there is a setting somewhere that could be activated for you but not
for me.

Best Regards,

Rodrigo Marino

On Thu, Mar 22, 2012 at 1:56 PM, Theresa Swayne <[hidden email]> wrote: