Macro to define a local region of interest

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Macro to define a local region of interest

Douglas Benn-2
I am creating an anatomical atlas of CTs and have a student laboriously
identifying anatomical points with a mouse click. I would like to use a
pair of x,y cords as a starting point to automatically search for a
region which has similar properties in terms of grayness which will
outline the anatomical structure such as the Maxillary sinus. Is there a
macro which if you give it a starting x,y coordinate will search around
to form a closed ROI?

 

Thanks!

 

Douglas

 

Dr Douglas K Benn, BDS, DDS, M.Phil., Ph.D., Dipl. Dental Radiology
(Royal College of Radiologists, England).

Professor and Director of Oral & Maxillofacial Radiology

Dept of General Dentistry, Room 210

Creighton University School of Dentistry

2802 Webster Street Omaha

Nebraska 68178

 

Tel: (402)280 5025

Fax: (402)280 5094

 
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Re: Macro to define a local region of interest

Nathaniel Ryckman
Benn, Douglas K. wrote
I am creating an anatomical atlas of CTs and have a student laboriously
identifying anatomical points with a mouse click. I would like to use a
pair of x,y cords as a starting point to automatically search for a
region which has similar properties in terms of grayness which will
outline the anatomical structure such as the Maxillary sinus. Is there a
macro which if you give it a starting x,y coordinate will search around
to form a closed ROI?

 

Thanks!

 

Douglas

 

Dr Douglas K Benn, BDS, DDS, M.Phil., Ph.D., Dipl. Dental Radiology
(Royal College of Radiologists, England).

Professor and Director of Oral & Maxillofacial Radiology

Dept of General Dentistry, Room 210

Creighton University School of Dentistry

2802 Webster Street Omaha

Nebraska 68178

 

Tel: (402)280 5025

Fax: (402)280 5094
I haven't used this plugin myself, but I heard the Versatile Wand is pretty good.

http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
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Re: Macro to define a local region of interest

Nathaniel Ryckman
In reply to this post by Douglas Benn-2
Benn, Douglas K. wrote
I am creating an anatomical atlas of CTs and have a student laboriously
identifying anatomical points with a mouse click. I would like to use a
pair of x,y cords as a starting point to automatically search for a
region which has similar properties in terms of grayness which will
outline the anatomical structure such as the Maxillary sinus. Is there a
macro which if you give it a starting x,y coordinate will search around
to form a closed ROI?

 

Thanks!

 

Douglas

 

Dr Douglas K Benn, BDS, DDS, M.Phil., Ph.D., Dipl. Dental Radiology
(Royal College of Radiologists, England).

Professor and Director of Oral & Maxillofacial Radiology

Dept of General Dentistry, Room 210

Creighton University School of Dentistry

2802 Webster Street Omaha

Nebraska 68178

 

Tel: (402)280 5025

Fax: (402)280 5094
Also, you could try the menu commands:

AutoThreshold or Threshold->Watershed->Particle Analyzer

Good luck!
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Re: Macro to define a local region of interest

Michael Schmid
In reply to this post by Douglas Benn-2
Hi Douglas,

you can do this with the Wand tool in ImageJ. The macro call is:

  doWand(x, y, tolerance, "8-connected")

where 'tolerance' specifies how much the gray value may deviate from the one at (x,y).

The 'versatile wand' plugin also allows you to specify a maximum gradient and can do selections with inner holes.

  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

Michael
____________________________________________________________________________


On 2011-Jun-01, at 18:47, Benn, Douglas K. wrote:

> I am creating an anatomical atlas of CTs and have a student laboriously
> identifying anatomical points with a mouse click. I would like to use a
> pair of x,y cords as a starting point to automatically search for a
> region which has similar properties in terms of grayness which will
> outline the anatomical structure such as the Maxillary sinus. Is there a
> macro which if you give it a starting x,y coordinate will search around
> to form a closed ROI?
>
> Thanks!
>
> Douglas
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Re: Macro to define a local region of interest

Douglas Benn-2
Dear Michael,

Excellent.

Much appreciated.

Thank you.

Douglas

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Michael Schmid
Sent: Wednesday, June 01, 2011 12:30 PM
To: [hidden email]
Subject: Re: Macro to define a local region of interest

Hi Douglas,

you can do this with the Wand tool in ImageJ. The macro call is:

  doWand(x, y, tolerance, "8-connected")

where 'tolerance' specifies how much the gray value may deviate from the
one at (x,y).

The 'versatile wand' plugin also allows you to specify a maximum
gradient and can do selections with inner holes.

 
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wan
d:start

Michael
________________________________________________________________________
____


On 2011-Jun-01, at 18:47, Benn, Douglas K. wrote:

> I am creating an anatomical atlas of CTs and have a student
laboriously
> identifying anatomical points with a mouse click. I would like to use
a
> pair of x,y cords as a starting point to automatically search for a
> region which has similar properties in terms of grayness which will
> outline the anatomical structure such as the Maxillary sinus. Is there
a
> macro which if you give it a starting x,y coordinate will search
around
> to form a closed ROI?
>
> Thanks!
>
> Douglas
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Re: Macro to define a local region of interest

Douglas Benn-2
In reply to this post by Michael Schmid
Hi Michael,

I ran doWand as an installed macro and it worked fine on an open image. Is it possible to save the region in the ROI Manager as a new item in a list?

Thanks.

Douglas

Dr Douglas K Benn, BDS,DDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal College of Radiologists, England).
Professor and Director of Oral & Maxillofacial Radiology
Dept of General Dentistry
Creighton University Dental School
2802 Webster St, Boyne 210
Omaha
Nebraska 68178

Tel: (402)280 5025
Fax: (402)280 5094



-----Original Message-----
From: ImageJ Interest Group on behalf of Michael Schmid
Sent: Wed 6/1/2011 12:29 PM
To: [hidden email]
Subject: Re: Macro to define a local region of interest
 
Hi Douglas,

you can do this with the Wand tool in ImageJ. The macro call is:

  doWand(x, y, tolerance, "8-connected")

where 'tolerance' specifies how much the gray value may deviate from the one at (x,y).

The 'versatile wand' plugin also allows you to specify a maximum gradient and can do selections with inner holes.

  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

Michael
____________________________________________________________________________


On 2011-Jun-01, at 18:47, Benn, Douglas K. wrote:

> I am creating an anatomical atlas of CTs and have a student laboriously
> identifying anatomical points with a mouse click. I would like to use a
> pair of x,y cords as a starting point to automatically search for a
> region which has similar properties in terms of grayness which will
> outline the anatomical structure such as the Maxillary sinus. Is there a
> macro which if you give it a starting x,y coordinate will search around
> to form a closed ROI?
>
> Thanks!
>
> Douglas
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Re: Macro to define a local region of interest

Douglas Benn-2
Dear Michael,

I found out how to do it.

Best wishes.

Douglas

Dr Douglas K Benn, BDS,DDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal College of Radiologists, England).
Professor and Director of Oral & Maxillofacial Radiology
Dept of General Dentistry
Creighton University Dental School
2802 Webster St, Boyne 210
Omaha
Nebraska 68178

Tel: (402)280 5025
Fax: (402)280 5094



-----Original Message-----
From: ImageJ Interest Group on behalf of Benn, Douglas K.
Sent: Wed 6/1/2011 8:53 PM
To: [hidden email]
Subject: Re: Macro to define a local region of interest
 
Hi Michael,

I ran doWand as an installed macro and it worked fine on an open image. Is it possible to save the region in the ROI Manager as a new item in a list?

Thanks.

Douglas

Dr Douglas K Benn, BDS,DDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal College of Radiologists, England).
Professor and Director of Oral & Maxillofacial Radiology
Dept of General Dentistry
Creighton University Dental School
2802 Webster St, Boyne 210
Omaha
Nebraska 68178

Tel: (402)280 5025
Fax: (402)280 5094



-----Original Message-----
From: ImageJ Interest Group on behalf of Michael Schmid
Sent: Wed 6/1/2011 12:29 PM
To: [hidden email]
Subject: Re: Macro to define a local region of interest
 
Hi Douglas,

you can do this with the Wand tool in ImageJ. The macro call is:

  doWand(x, y, tolerance, "8-connected")

where 'tolerance' specifies how much the gray value may deviate from the one at (x,y).

The 'versatile wand' plugin also allows you to specify a maximum gradient and can do selections with inner holes.

  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

Michael
____________________________________________________________________________


On 2011-Jun-01, at 18:47, Benn, Douglas K. wrote:

> I am creating an anatomical atlas of CTs and have a student laboriously
> identifying anatomical points with a mouse click. I would like to use a
> pair of x,y cords as a starting point to automatically search for a
> region which has similar properties in terms of grayness which will
> outline the anatomical structure such as the Maxillary sinus. Is there a
> macro which if you give it a starting x,y coordinate will search around
> to form a closed ROI?
>
> Thanks!
>
> Douglas