[Chimera-users] Regarding estimation of volume in 2D

Tom Goddard 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.
>     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 at gmail.com <mailto:poornima.josyula at gmail.com>
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