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Re: [shapeworks-users] Shapeworks does not seem to properly place particles on specimens with different sizes. How can we fix that?


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  • From: "Savriama, Yoland F" <yoland.savriama@helsinki.fi>
  • To: Praful Agrawal <prafulag@cs.utah.edu>, "shapeworks-users@sci.utah.edu" <shapeworks-users@sci.utah.edu>
  • Subject: Re: [shapeworks-users] Shapeworks does not seem to properly place particles on specimens with different sizes. How can we fix that?
  • Date: Mon, 15 May 2017 15:17:17 +0000
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Hi Praful,


Thanks for getting in touch. Here are the snapshots of the parameters for Grooming and Optimize.


Best,

Yoland

From: Praful Agrawal <prafulag@cs.utah.edu>
Sent: Monday, May 15, 2017 5:49:44 PM
To: shapeworks-users@sci.utah.edu; Savriama, Yoland F
Subject: Re: [shapeworks-users] Shapeworks does not seem to properly place particles on specimens with different sizes. How can we fix that?
 
Hi Yoland,

Please share the snapshot of Optimization tab with parameters, it could be very helpful in debugging these results.

Thanks,
Praful
On May 15, 2017, at 8:39 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi> wrote:


Greetings,

I have been recently using the latest version of ShapeWorksStudio on a Mac Book Pro with Mac Os X 10.16.6 and I am dealing with brains of snakes and lizards. The volumes have been reconstructed and aligned with Amira. In our dataset, brains can have very different shapes and also very different sizes. When I use 200 particles placed on a couple of specimens, it is obvious that the coverage is more than enough for the smallest specimen, and it is problematic for the much larger one since it is clear that the coverage is not the same for both specimens. 

Please see attached screenshots that illustrate this issue.

I was wondering if all specimens have to be somehow scaled to a common unit size such that they can properly treated in ShapeWorks? If so, could you explain to me the procedure for this scaling in Amira, please?

Also, does the color of particles have a meaning? For instance, does the color reflect the "homology" in placing a given particle on different surfaces?

Best wishes,
Yoland Savriama, PhD
P/O Jernvall
Institute of Biotechnology
P.O. Box 56 (Viikinkaari 5)
FIN-00014 FINLAND

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