3D animation software
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi everyone, What kind of 3D reconstruction software do you use to demonstrate your 3-D confocal data? How is its performance to grayscale/color image stacks? Thank you! Best, Peng Xi Dantus Research Group Department of Chemistry Michigan State University East Lansing, MI 48824 Tel: (517) 355-9715 x319 Email: [hidden email] http://www.msu.edu/~xipeng/ |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear Peng Xi, If its just for displaying you can used Voxx, its free for non-commercial use! and the (free) most stable I've tested up to now. Regards, NM Peng Xi wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi everyone, > What kind of 3D reconstruction software do you use to demonstrate > your 3-D confocal data? How is its performance to grayscale/color image > stacks? Thank you! > > Best, > Peng Xi > Dantus Research Group > Department of Chemistry > Michigan State University > East Lansing, MI 48824 > Tel: (517) 355-9715 x319 > Email: [hidden email] > http://www.msu.edu/~xipeng/ > -- Nuno Moreno Cell Imaging Unit Instituto Gulbenkian de Ciência http://uic.igc.gulbekian.pt http://www.igc.gulbekian.pt phone +351 214464606 fax +351 214407970 |
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In reply to this post by Peng Xi-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi, I like to use Amira (www.amiravis.com). About performance I cannot say much, as I have not really worked with other packages. A modern PC works nice with it (2-3 years ago drinking coffee got a bad habit). If you have an "old" CRT monitor and a graphics adapter supporting 3D in OpenGL (like an Nvidia Quadro card), you can use old PC stereo shutter glasses like Elsa's Revelator (cheap at eBay) to view your data in 3D. You can export your data to VRML files. Adobe Acrobat 3D (Version 8, not 7) can import these files, and then you just have a "normal" pdf file which can be opend on any computer with Acrobat Reader 8, and you can rotate you neurons, molecules or whatever in all directions. Hope this helps. :-) Torsten P.S. No commercial interests, just a happy user (most of the time)... On 8 Oct 2007 at 9:46, Peng Xi wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi everyone, > What kind of 3D reconstruction software do you use to demonstrate > your 3-D confocal data? How is its performance to grayscale/color image > stacks? Thank you! > > Best, > Peng Xi Torsten Fregin Universität Hamburg - Zoologisches Institut Abt. Neurophysiologie AG Wiese - Raum 413 Martin-Luther-King-Platz 3 20146 Hamburg, Germany Telefon *49-(0)40-42838-3931 Fax *49-(0)40-42838-3937 eMail [hidden email] [hidden email] |
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In reply to this post by Peng Xi-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Are any of these systems good at displaying multi-channel data? We have some 5-channel datasets, and we hope to progress to more channels some day. Badri Roysam Professor, Department of Electrical, Computer and Systems Engineering Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC) Rensselaer Polytechnic Institute 110 8th Street, Troy, New York 12180-3590. Office(JEC 7010): 518-276-8067, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715 Email: [hidden email], Web: http://www.ecse.rpi.edu/~roysam ----- Original Message ----- From: Torsten Fregin [mailto:[hidden email]] To: [hidden email] Subject: Re: 3D animation software > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi, > > I like to use Amira (www.amiravis.com). About performance I cannot say much, > as I have not > really worked with other packages. A modern PC works nice with it (2-3 years > ago drinking > coffee got a bad habit). If you have an "old" CRT monitor and a graphics > adapter supporting > 3D in OpenGL (like an Nvidia Quadro card), you can use old PC stereo shutter > glasses like > Elsa's Revelator (cheap at eBay) to view your data in 3D. > > You can export your data to VRML files. Adobe Acrobat 3D (Version 8, not 7) > can import > these files, and then you just have a "normal" pdf file which can be opend > on any computer > with Acrobat Reader 8, and you can rotate you neurons, molecules or whatever > in all > directions. > > Hope this helps. > > :-) Torsten > > P.S. No commercial interests, just a happy user (most of the time)... > > > On 8 Oct 2007 at 9:46, Peng Xi wrote: > > > Search the CONFOCAL archive at > > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > > > Hi everyone, > > What kind of 3D reconstruction software do you use to demonstrate > > your 3-D confocal data? How is its performance to grayscale/color image > > stacks? Thank you! > > > > Best, > > Peng Xi > > > Torsten Fregin > > Universität Hamburg - Zoologisches Institut > Abt. Neurophysiologie > AG Wiese - Raum 413 > Martin-Luther-King-Platz 3 > 20146 Hamburg, Germany > Telefon *49-(0)40-42838-3931 > Fax *49-(0)40-42838-3937 > eMail [hidden email] > [hidden email] > |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Do you see this??
You are invited to attend a live, interactive, web-based instructional seminar:
==============================================================
"3D Reconstruction and Presentation of Microscopy Images"
Presented by Bartek Rajwa, Ph.D.
Purdue University Cytometry Laboratories
Sponsored by Media Cybernetics and QImaging
================================================= ============= Details are below. Connection lines are limited, so reserve yours now. There is no charge to participate in this on-line seminar.
When:
Thursday, 11-October, 1:00PM (
Eastern time; 10 AM Pacific time)
Duration: Approximately 1 hour.
Pre-register (required) at: https://mediacy.webex.com/mediacy/j.php?ED=2412243&RG=1 [If this link has wrapped, please re-build it in your web browser's address bar. The line begins with "https" and ends with " RG=1" ] Details:
=====================
Modern optical microscopy provides powerful tools for studying biological samples varying from sub-cellular structures to tissues. Transforming complex, multidimensional microscopy data sets into the actual presentation for use in lectures, web sites, or published materials requires not only knowledge about digital image acquisition and image processing but also familiarity with visualization techniques.
Attendees will learn various approaches to multidimensional data visualization of microscopy images
and will see examples of software tools available for these tasks.
Specifically, the workshop will address the following topics:
Sponsored by Media Cybernetics
(Image Pro and AutoQuant software) and QImaging (
digital cameras for microscopy)
This seminar requires that attendees use a Java-enabled browser with a high bandwidth connection. Audio is via telephone.
Long distance toll charges may apply. There is no charge to participate in this on-line seminar. On 10/8/07, Badri Roysam <[hidden email]> wrote:
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In reply to this post by Peng Xi-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Could you define to what you are referring? Brightest point projections, projections with alpha rendering, surface rendering, solid models, etc. Grayscale presentation of individual channels is often advantageous. The human eye is weakly sensitive to blue, and lacks blue cones in the fovea. Thus the 'blue' channel will appear dim and lacking detail. Changing the blue LUT to cyan helps greatly overcome the problem. Often the channels will obscure one another, so you may want to display one or more channels as grayscale in order to obtain a clear presentation of details. Using the a monochrome display in conjunction with an RGB display allows presenting both the details and the overall contextual image without needing to distort the histogram to make an obscured channel equally visible in an RGB presentation. Glen MacDonald Core for Communication Research Virginia Merrill Bloedel Hearing Research Center Box 357923 University of Washington Seattle, WA 98195-7923 USA (206) 616-4156 [hidden email] ************************************************************************ ****** The box said "Requires WindowsXP or better", so I bought a Macintosh. ************************************************************************ ****** On Oct 8, 2007, at 6:46 AM, Peng Xi wrote: Regards, Glen > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi everyone, > What kind of 3D reconstruction software do you use to > demonstrate your 3-D confocal data? How is its performance to > grayscale/color image stacks? Thank you! > > Best, > Peng Xi > Dantus Research Group > Department of Chemistry > Michigan State University > East Lansing, MI 48824 > Tel: (517) 355-9715 x319 > Email: [hidden email] > http://www.msu.edu/~xipeng/ |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Glen, I mean all (Brightest point projections, projections with alpha rendering, surface rendering, solid models, etc.) possible presentation menthods for a presentation of an image stack (currently I am working on one channel only but it can be 2-3 colors in future). So far I've got a lot of feedbacks with many softwares I've never aware of. It will take me sometime to test them out. :) Thank you! Best, Peng Dantus Research Group Department of Chemistry Michigan State University East Lansing, MI 48824 Tel: (517) 355-9715 x319 Email: [hidden email] http://www.msu.edu/~xipeng/ Glen MacDonald wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Could you define to what you are referring? Brightest point > projections, projections with alpha rendering, surface rendering, > solid models, etc. > Grayscale presentation of individual channels is often advantageous. > The human eye is weakly sensitive to blue, and lacks blue cones in the > fovea. Thus the 'blue' channel will appear dim and lacking detail. > Changing the blue LUT to cyan helps greatly overcome the problem. > Often the channels will obscure one another, so you may want to > display one or more channels as grayscale in order to obtain a clear > presentation of details. Using the a monochrome display in > conjunction with an RGB display allows presenting both the details and > the overall contextual image without needing to distort the histogram > to make an obscured channel equally visible in an RGB presentation. > Glen MacDonald > Core for Communication Research > Virginia Merrill Bloedel Hearing Research Center > Box 357923 > University of Washington > Seattle, WA 98195-7923 USA > (206) 616-4156 > [hidden email] > > ****************************************************************************** > > The box said "Requires WindowsXP or better", so I bought a Macintosh. > ****************************************************************************** > > > > On Oct 8, 2007, at 6:46 AM, Peng Xi wrote: > > Regards, > Glen > >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> Hi everyone, >> What kind of 3D reconstruction software do you use to demonstrate >> your 3-D confocal data? How is its performance to grayscale/color >> image stacks? Thank you! >> >> Best, >> Peng Xi >> Dantus Research Group >> Department of Chemistry >> Michigan State University >> East Lansing, MI 48824 >> Tel: (517) 355-9715 x319 >> Email: [hidden email] >> http://www.msu.edu/~xipeng/ > |
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In reply to this post by Peng Xi-2
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Commercial Interest. Andor Technology offers its own Andor iQ software that is unparalleled for rendering large multi-dimensional data sets, due to its unique memory manager. While not freeware, it is very competitively priced. More information or a demo license can be obtained at the website, or by contacting myself. Thanks, Scott Phillips Imaging Applications Specialist [hidden email] 206-280-5597 Andor Technology Web: www.andor.com Main US Office: 860-290-9211 |
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