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

Tom Goddard goddard at sonic.net
Tue Dec 13 15:48:06 PST 2011

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 
> 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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> Chimera-users at cgl.ucsf.edu
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