Regarding estimation of volume in 2D
Respected Sir/Madam, My name is Poornima and I am a Ph.D. student from India. My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels. I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately. Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out. Is there a way Chimera can help me estimate this volume? Please let me know your suggestions. Thank you for your time and patience in reading my mail, despite your busy schedule. Kindly excuse me for any inconvenience caused. Look forward to receive a positive response at the earliest. Have a good day. -- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula@gmail.com
Hi Poornima, Sorry, I can't think of how to make that measurement using Chimera. The volume calculation in Chimera works with 3D isosurfaces. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 12, 2011, at 8:50 PM, Poornima Josyula wrote:
Respected Sir/Madam,
My name is Poornima and I am a Ph.D. student from India.
My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels.
I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately.
Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out.
Is there a way Chimera can help me estimate this volume?
Please let me know your suggestions.
Thank you for your time and patience in reading my mail, despite your busy schedule.
Kindly excuse me for any inconvenience caused.
Look forward to receive a positive response at the earliest.
Have a good day.
-- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula@gmail.com
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Hi Poornima, I'm sure ImageJ can do this better than Chimera because ImageJ is aimed at 2d image analysis and Chimera is intended for 3d image analysis. Still it can be done in Chimera. I made your image background black, then switched to grayscale in Gimp. Chimera can open a grayscale tiff but not a color one. Then I used the Measure and Color Blobs tool (menu Tools / Volume Data) to find that the area you showed in red is about 9000 pixels. Depends exactly where you set the threshold because your red blends smoothly into yellow. Tom
Respected Sir/Madam,
My name is Poornima and I am a Ph.D. student from India.
My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels.
I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately.
Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out.
Is there a way Chimera can help me estimate this volume?
Please let me know your suggestions.
Thank you for your time and patience in reading my mail, despite your busy schedule.
Kindly excuse me for any inconvenience caused.
Look forward to receive a positive response at the earliest.
Have a good day.
-- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula@gmail.com <mailto:poornima.josyula@gmail.com>
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Oops, should be 4500 pixels. The area Chimera is the for a flat 3d surface that is closed (ie has 2 sides) so the 9000 represents area of both top and bottom sides. Tom
Hi Poornima,
I'm sure ImageJ can do this better than Chimera because ImageJ is aimed at 2d image analysis and Chimera is intended for 3d image analysis. Still it can be done in Chimera. I made your image background black, then switched to grayscale in Gimp. Chimera can open a grayscale tiff but not a color one. Then I used the Measure and Color Blobs tool (menu Tools / Volume Data) to find that the area you showed in red is about 9000 pixels. Depends exactly where you set the threshold because your red blends smoothly into yellow.
Tom
Respected Sir/Madam,
My name is Poornima and I am a Ph.D. student from India.
My area of research is Biofluid Mechanics. I am modeling bubble transport in bifurcating microchannels.
I am performing 2D simulations for the above problem using a commercial Computational Fluid Dynamics (CFD) software called ANSYS Fluent. ImageJ is currently used for the purpose of post processing. But, I haven't entirely been successful in estimating the volume accurately.
Please find attached a snapshot of the simulation. In that snapshot, my region of interest (ROI) is the red colored area whose volume I have to find out.
Is there a way Chimera can help me estimate this volume?
Please let me know your suggestions.
Thank you for your time and patience in reading my mail, despite your busy schedule.
Kindly excuse me for any inconvenience caused.
Look forward to receive a positive response at the earliest.
Have a good day.
-- With best regards, Poornima Josyula Ph.D. Scholar Fluid Mechanics Laboratory Dept. of Applied Mechanics IIT, Madras India E-mail: poornima.josyula@gmail.com <mailto:poornima.josyula@gmail.com>
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participants (3)
-
Elaine Meng -
Poornima Josyula -
Tom Goddard