shapeworks-users

Text archives Help


Re: [shapeworks-users] Shapeworks


Chronological Thread 
  • From: Alan Morris <alan.morris@utah.edu>
  • To: "Barnet, Isabel" <ibarnet@hms.harvard.edu>, Shireen Elhabian <shireen@sci.utah.edu>, "Beroukhim, Rebecca" <Rebecca.Beroukhim@CARDIO.CHBOSTON.ORG>
  • Cc: Shireen Elhabian <shireen@sci.utah.edu>, "shapeworks-users@sci.utah.edu" <shapeworks-users@sci.utah.edu>
  • Subject: Re: [shapeworks-users] Shapeworks
  • Date: Wed, 22 Nov 2023 16:08:07 +0000
  • Accept-language: en-US
  • Arc-authentication-results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=utah.edu; dmarc=pass action=none header.from=utah.edu; dkim=pass header.d=utah.edu; arc=none
  • Arc-message-signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-AntiSpam-MessageData-ChunkCount:X-MS-Exchange-AntiSpam-MessageData-0:X-MS-Exchange-AntiSpam-MessageData-1; bh=RdiJP4eFHuEdmljjBbaNCVNvmlQv3JhpAV9dBkTpLck=; b=bYZSOmO9FFHNQLIOe77oZPuJ934oBXD3JkUbrza4yHJZ2PK72v985MDg9vHzZYRkr6vQF/OMwcoYrMfthXUEgGqhfehy2XvHksW3ZRYQx+9xnqgudvhABYUfov3ablWlnEOLLcjkxs3zLx2Iiwl2SLgwhiY7qTmsgXc9ZKi1Q3Q9oRaRpur8QfBVzWE7ceaLxhxx/ckXbgNX0yeVlnP0TRyM6Rd8pPmrhAKF0vrn8pMeDs8+ykOptkPOYB+59CkAcdrZbZUI/E8SXwmvhTnmCCVMT9bbdI8omTgMZsBdXtnaGkZCgUfQBatmob+C4VSTPeJD9OFgwsA6TNZ4A3OWPA==
  • Arc-seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=nzWUhH1BiebWYYe4aJ/sCrlkrGYzVwa0tSmHl3TyPnFfcZJmcvIUeLst0ME4hJI+rUX0iqQcAIcomWPaaAKvH2FvWNOwRoTlrEpHIOlH+EJKM3em4Z8jpfIoVjY9rrJqdlkU1DOPgY5nvRlZlFXJCE9FhJXydRMBHG7yY+a3kKcmJTm4EXKdHFp848zkIVR1EpiV6UBiHGwJBz7WKcOMTFRuX5eTENnkJKy+88yU/FUTB88a1iQfZ6DAc6ix0MppN6ckNBZeoT/OKuE31oZA+hQbfCcWNHcb5cSlPxf9GRSTrofvfr7c6yHfIYowWAY6Ac/wz6nIC5cPu4fdxZcYnA==
  • Authentication-results: dkim=none (message not signed) header.d=none;dmarc=none action=none header.from=utah.edu;

Isabel,

 

Yes, the PCA montage export will use the same settings from the main viewer.  Simply turn off particle display:

 

 

Then the export will not show particles either:

 

Thanks,

Alan

 

 

From: Barnet, Isabel <ibarnet@hms.harvard.edu>
Date: Wednesday, November 22, 2023 at 7:02 AM
To: Shireen Elhabian <shireen@sci.utah.edu>, Beroukhim, Rebecca <Rebecca.Beroukhim@CARDIO.CHBOSTON.ORG>
Cc: Shireen Elhabian <shireen@sci.utah.edu>, shapeworks-users@sci.utah.edu <shapeworks-users@sci.utah.edu>, Alan Morris <amorris@sci.utah.edu>
Subject: Re: Shapeworks

Hello,

 

I hope all is well! I am working on exporting images from our principal component analysis in ShapeWorks. Is there an easy way to export a PCA montage of shapes without their overlaying particles? I could not find any information in existing documentation.

 

Thank you, and Happy Thanksgiving!

 

Best,

Isabel

 

From: Shireen Elhabian <shireen@sci.utah.edu>
Date: Tuesday, October 17, 2023 at 6:32 PM
To: Beroukhim, Rebecca <Rebecca.Beroukhim@CARDIO.CHBOSTON.ORG>
Cc: Shireen Elhabian <shireen@sci.utah.edu>, shapeworks-users@sci.utah.edu <shapeworks-users@sci.utah.edu>, Barnet, Isabel <ibarnet@hms.harvard.edu>, Alan Morris <amorris@sci.utah.edu>
Subject: Re: Shapeworks

Hi Rebecca,

 

The question is a bit ambiguous. Are you referring to the corresponding particles, or the various analytical outcomes? This could include reconstructed shapes, PCA loadings, or DeepSSM results.

 

To best address this, I'd suggest checking out the analysis documentation page.

 

Please let us know if you have further questions.

 

Regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Associate Professor of Computer Science 
Scientific Computing and Imaging Institute
Kahlert School of Computing
University of Utah
WEB 3608
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 581-5982

Fax (801) 585-6513
Home Page: http://www.sci.utah.edu/~shireen




On Oct 17, 2023, at 11:11 AM, Beroukhim, Rebecca <Rebecca.Beroukhim@CARDIO.CHBOSTON.ORG> wrote:

 

Hi, we are wondering if you have a user manual for Shapeworks that includes a description of the output?

 

Thank you

Rebecca 

 

PNG image

PNG image


  • Re: [shapeworks-users] Shapeworks, Alan Morris, 11/22/2023

Archive powered by MHonArc 2.6.18.

Top of page