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 |
In reply to this post by Douglas Benn-2
Also, you could try the menu commands: AutoThreshold or Threshold->Watershed->Particle Analyzer Good luck! |
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 |
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 |
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 |
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 |
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