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Hello!
I am trying to count small bright objects included in larger less intense somewhat spherical objects. Using the 3D Objects Counter in FIJI/Analyze I can get nice identification and counts of the larger 3D objects. Now it would seem easy to make each of them a region of interest but I am at a loss on how to do it. Below is an orthogonal cut through the top orange object to give an idea of how this looks. Anyone can please help? Thank you so very much! Anda Anda Cornea, Ph.D. Director of the Imaging and Morphology Support Core Oregon National Primate Research Center OHSU 503-690-5293 [cid:image001.png@01CEB554.BDB85E60] [cid:image002.png@01CEB554.BDB85E60] [cid:image003.png@01CEB554.BDB85E60] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html ![]() ![]() ![]() |
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Hi Anda,
You can use the 3DRoiManager, which can display Rois of 3D objects in selected slices. I can send you macros for automation if you are interested. http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start best, Thomas Le 20/09/2013 01:28, Anda Cornea a écrit : > Hello! > > > > I am trying to count small bright objects included in larger less intense somewhat spherical objects. Using the 3D Objects Counter in FIJI/Analyze I can get nice identification and counts of the larger 3D objects. Now it would seem easy to make each of them a region of interest but I am at a loss on how to do it. Below is an orthogonal cut through the top orange object to give an idea of how this looks. Anyone can please help? > > > > Thank you so very much! > > > Anda > > > > Anda Cornea, Ph.D. > Director of the Imaging and Morphology Support Core > Oregon National Primate Research Center > OHSU > 503-690-5293 > > > > > > > [cid:image001.png@01CEB554.BDB85E60] [cid:image002.png@01CEB554.BDB85E60] > > > > > > [cid:image003.png@01CEB554.BDB85E60] > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > ... [show rest of quote] -- /**********************************************************/ Thomas Boudier, MCU Université Pierre et Marie Curie, Modélisation Cellulaire et Imagerie Biologique (EE1), IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu. Tel : 01 44 27 46 92 Fax : 01 44 27 22 91 /*******************************************************/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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I think that this is exactly what I was looking for, thank you so much! I'll give it a try and see if I need more automation. It is so awesome that you would offer.
Best wishes, Anda Sent from my iPad On Sep 20, 2013, at 12:41 AM, "Thomas Boudier" <[hidden email]> wrote: > Hi Anda, > > You can use the 3DRoiManager, which can display Rois of 3D objects in > selected slices. I can send you macros for automation if you are interested. > > http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start > > best, > > Thomas > > > Le 20/09/2013 01:28, Anda Cornea a écrit : >> Hello! >> >> >> >> I am trying to count small bright objects included in larger less intense somewhat spherical objects. Using the 3D Objects Counter in FIJI/Analyze I can get nice identification and counts of the larger 3D objects. Now it would seem easy to make each of them a region of interest but I am at a loss on how to do it. Below is an orthogonal cut through the top orange object to give an idea of how this looks. Anyone can please help? >> >> >> >> Thank you so very much! >> >> >> Anda >> >> >> >> Anda Cornea, Ph.D. >> Director of the Imaging and Morphology Support Core >> Oregon National Primate Research Center >> OHSU >> 503-690-5293 >> >> >> >> >> >> >> [cid:image001.png@01CEB554.BDB85E60] [cid:image002.png@01CEB554.BDB85E60] >> >> >> >> >> >> [cid:image003.png@01CEB554.BDB85E60] >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > /**********************************************************/ > Thomas Boudier, MCU Université Pierre et Marie Curie, > Modélisation Cellulaire et Imagerie Biologique (EE1), > IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu. > Tel : 01 44 27 46 92 Fax : 01 44 27 22 91 > /*******************************************************/ > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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