[Chimera-users] Regarding estimation of volume in 2D
goddard at sonic.net
Tue Dec 13 16:02:38 PST 2011
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.
> 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.
>> 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
>> 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
>> E-mail: poornima.josyula at gmail.com <mailto:poornima.josyula at gmail.com>
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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