measurement within outlined area

[ANDREI SDRULLA]

Hi,

I have z-stacks of 8 bit grayscale images that have structures (cells) outlined by hand (they're outlined by hand because thresholding doesn't work well).  I want to get measurements of the area outlined, mean pixel value, sum of all pixels within the outline, etc..  Any ideas/plugins on how to do this?

Thanks in advance,

Andrei

[Ludgate, David]

All these are possible, if you can select the outlined cell (create a
roi around it). As for how to do this automatically, you could look at
the wand tool, or perhaps analyze particles. I've had success with
inverting an image so that white areas look like black particles, then
using particle analyzer to get measurements on that area.
dave

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
ANDREI SDRULLA
Sent: Monday, August 15, 2005 1:01 PM
To: [hidden email]
Subject: measurement within outlined area


Hi,

I have z-stacks of 8 bit grayscale images that have structures (cells)
outlined by hand (they're outlined by hand because thresholding doesn't
work well).  I want to get measurements of the area outlined, mean pixel
value, sum of all pixels within the outline, etc..  Any ideas/plugins on
how to do this?

Thanks in advance,

Andrei

[ANDREI SDRULLA]

The problem is that i'm not sure how to outline the outline :)  You're right, inverting the image and then using the wand tool is a possibilty; then I have to invert it again, plus it doesn't give me a lot of flexibility in terms of what I can measure.  I'll probably have to do it though unless I figure something else out..

Thanks,
andrei

----- Original Message -----
From: "Ludgate, David" <[hidden email]>
Date: Monday, August 15, 2005 4:18 pm
Subject: Re: measurement within outlined area

> All these are possible, if you can select the outlined cell (create a
> roi around it). As for how to do this automatically, you could look at
> the wand tool, or perhaps analyze particles. I've had success with
> inverting an image so that white areas look like black particles, then
> using particle analyzer to get measurements on that area.
> dave
>
> -----Original Message-----
> From: ImageJ Interest Group [[hidden email]] On Behalf Of
> ANDREI SDRULLA
> Sent: Monday, August 15, 2005 1:01 PM
> To: [hidden email]
> Subject: measurement within outlined area
>
>
> Hi,
>
> I have z-stacks of 8 bit grayscale images that have structures (cells)
> outlined by hand (they're outlined by hand because thresholding
> doesn'twork well).  I want to get measurements of the area
> outlined, mean pixel
> value, sum of all pixels within the outline, etc..  Any
> ideas/plugins on
> how to do this?
>
> Thanks in advance,
>
> Andrei
>

[W. Chan]

Hi Andrei

If your outline is distinct from your image e.g., the outline is 255 and
nothing in your sample is 255 then simply select the wand tool and click
on the outline will have it selected.  Then you can threshold the image
but restrict the range so it does not cover 255.  If you run particle
analysis, it should be done on the structure but not the outline.

If you hold down the shift key while applying the wand, you can select
multiple outlines.  Blowing up the image may facilitate cursor placement
while using the wand.  Or you can use the ROI manager tool to combine
multiple ROI.  Good luck.

--
Pang (Wai Pang Chan, [hidden email])

On Mon, 15 Aug 2005, ANDREI SDRULLA wrote:

> The problem is that i'm not sure how to outline the outline :)  You're
> right, inverting the image and then using the wand tool is a possibilty;
> then I have to invert it again, plus it doesn't give me a lot of
> flexibility in terms of what I can measure.  I'll probably have to do it
> though unless I figure something else out..
>
> Thanks,
> andrei
>
> ----- Original Message -----
> From: "Ludgate, David" <[hidden email]>
> Date: Monday, August 15, 2005 4:18 pm
> Subject: Re: measurement within outlined area
>
>> All these are possible, if you can select the outlined cell (create a
>> roi around it). As for how to do this automatically, you could look at
>> the wand tool, or perhaps analyze particles. I've had success with
>> inverting an image so that white areas look like black particles, then
>> using particle analyzer to get measurements on that area.
>> dave
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [[hidden email]] On Behalf Of
>> ANDREI SDRULLA
>> Sent: Monday, August 15, 2005 1:01 PM
>> To: [hidden email]
>> Subject: measurement within outlined area
>>
>>
>> Hi,
>>
>> I have z-stacks of 8 bit grayscale images that have structures (cells)
>> outlined by hand (they're outlined by hand because thresholding
>> doesn'twork well).  I want to get measurements of the area
>> outlined, mean pixel
>> value, sum of all pixels within the outline, etc..  Any
>> ideas/plugins on
>> how to do this?
>>
>> Thanks in advance,
>>
>> Andrei
>>
>