I am still slowly plodding through ROIs and ROImanager.
I am able to make a jpg copy of a ROI of interest but the most right column and the most inferior row of pixels are not saved using the code roiManager("select", i); run("Duplicate..."); saveAs("Jpeg"); Is there a way of fixing this? Also what is the data stored by a .roi file? Thank you. Dr Douglas K Benn, BDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal College of Radiologists, England). Professor 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 |
Hi Douglas,
the problem is NOT partial copying on "Duplicate", it is just the way how ROIs are displayed on the screen. At 100% zoom, the yellow outline is inside the ROI at the top&left, outside the ROI at the bottom&right. At higher zoom levels (say, 400%), this 1-pixel-shift is less noticeable. It is the same for the outline created by typing CTRL-D (Draw), irrespective of the zoom level. Michael ________________________________________________________________ On 19 Apr 2010, at 23:17, Benn, Douglas K. wrote: > I am still slowly plodding through ROIs and ROImanager. > > > > I am able to make a jpg copy of a ROI of interest but the most right > column and the most inferior row of pixels are not saved using the > code > > > > roiManager("select", i); > > run("Duplicate..."); > > saveAs("Jpeg"); > > > > Is there a way of fixing this? > > > > Also what is the data stored by a .roi file? > > > > Thank you. > > > > > > Dr Douglas K Benn, BDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal > College of Radiologists, England). > > Professor > > 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 > > |
Dear Michael,
If I understand you correctly, the ROI outline is correctly stored in the form of a continuous loop and it is the display which gives the appearance of an incomplete loop? I will copy this to Wayne as he is looking into the problem for me. Very helpful. Thank you. 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 4/21/2010 2:52 AM To: [hidden email] Subject: Re: jpg copy of ROI Hi Douglas, the problem is NOT partial copying on "Duplicate", it is just the way how ROIs are displayed on the screen. At 100% zoom, the yellow outline is inside the ROI at the top&left, outside the ROI at the bottom&right. At higher zoom levels (say, 400%), this 1-pixel-shift is less noticeable. It is the same for the outline created by typing CTRL-D (Draw), irrespective of the zoom level. Michael ________________________________________________________________ On 19 Apr 2010, at 23:17, Benn, Douglas K. wrote: > I am still slowly plodding through ROIs and ROImanager. > > > > I am able to make a jpg copy of a ROI of interest but the most right > column and the most inferior row of pixels are not saved using the > code > > > > roiManager("select", i); > > run("Duplicate..."); > > saveAs("Jpeg"); > > > > Is there a way of fixing this? > > > > Also what is the data stored by a .roi file? > > > > Thank you. > > > > > > Dr Douglas K Benn, BDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal > College of Radiologists, England). > > Professor > > 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 > > |
On Wednesday 21 Apr 2010 16:27:55 you wrote:
> If I understand you correctly, the ROI outline is correctly stored in the > form of a continuous loop and it is the display which gives the appearance > of an incomplete loop? If this relates to cropped ROIs not showing the whole previously drawn outline (produced with the Draw command), then I believe this is something related to what we have been discussing in the fij-devel list recently (so those interested could see the thread through google-groups). I think that there are a number of relations between ROI (yellow frame), the inside, boundary and filled blobs, their areas and perimeters that could be handled in a more intuitive way and that would fulfill other expected relations useful for morphological operations. I understand that it might not be practical to change IJ behaviour now but Dscho suggested that this could be included in a ROI superclass that ImageJ2 or fiji could support in the future. That would be ideal. Cheers, G. |
Dear Gabriel,
Thank you for your comment. I will look up the list you mentioned. 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 Gabriel Landini Sent: Wed 4/21/2010 10:50 AM To: [hidden email] Subject: Re: jpg copy of ROI On Wednesday 21 Apr 2010 16:27:55 you wrote: > If I understand you correctly, the ROI outline is correctly stored in the > form of a continuous loop and it is the display which gives the appearance > of an incomplete loop? If this relates to cropped ROIs not showing the whole previously drawn outline (produced with the Draw command), then I believe this is something related to what we have been discussing in the fij-devel list recently (so those interested could see the thread through google-groups). I think that there are a number of relations between ROI (yellow frame), the inside, boundary and filled blobs, their areas and perimeters that could be handled in a more intuitive way and that would fulfill other expected relations useful for morphological operations. I understand that it might not be practical to change IJ behaviour now but Dscho suggested that this could be included in a ROI superclass that ImageJ2 or fiji could support in the future. That would be ideal. Cheers, G. |
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