3D printing
Locked
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hello all, Has anyone tried exporting a surface rendering from Huygens, Imaris, Volocity, Vaa3D etc for 3D printing? This is mostly a vanity exercise for cool desk art, but aside from that I suspect that there is non-zero analytical value in holding a structure in your hands. best, Tim Timothy Feinstein, Ph.D. | Manager, Core for Confocal Microscopy and Quantitative Imaging 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 Phone: 616-234-5819 | Email: [hidden email]<mailto:[hidden email]> |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Dear Tim, We have in fact done this on several scales using STED images surface rendered in Huygens. We then pass them through Imaris to generate an STL file and print them on a Makerbot. In the future it would be great to have an STL file format option in Huygens (hint, hint). We are visualizing F-actin and, while it definitely generates great desk art, there is also (as you put it) a non-zero analytical value of being able to pick it up and look at it. In order to maximize this we are playing with using dissolvable filament for the base and "filler", so we can really see fine structure in 3D. We have put up one of our models on the 3D print exchange here: http://3dprint.nih.gov/discover/3dpx-000748. It's broken into 4 components to keep the file size manageable. I'm happy to discuss details further if you like-- it's a fun exercise! Emily Emily Mace Senior Postdoctoral Fellow, PhD Laboratory of Jordan S. Orange, M.D., Ph.D. Center for Human Immunobiology Feigin Center 1102 Bates St Baylor College of Medicine and Texas Children's Hospital Houston, Texas, USA Cell: 267-746-1843 ________________________________________ From: Confocal Microscopy List <[hidden email]> on behalf of Feinstein, Timothy <[hidden email]> Sent: Wednesday, January 7, 2015 10:03 AM To: [hidden email] Subject: 3D printing ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hello all, Has anyone tried exporting a surface rendering from Huygens, Imaris, Volocity, Vaa3D etc for 3D printing? This is mostly a vanity exercise for cool desk art, but aside from that I suspect that there is non-zero analytical value in holding a structure in your hands. best, Tim Timothy Feinstein, Ph.D. | Manager, Core for Confocal Microscopy and Quantitative Imaging 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 Phone: 616-234-5819 | Email: [hidden email]<mailto:[hidden email]> |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Thanks Emily! It turns out that Huygens does not support any export of its surface rendering, at least not officially, but Imaris lets you export its rendering as a VRML2 file. However at least in Imaris 7.4 you need to manually edit the exported file extension from .vrml to .wrl before software like Blender can open it and convert it to a .stl file for 3D printing. I should note that Imaris is priced as a relatively niche product and it would still be helpful to know if this can be done using free software like Fiji or Vaa3d. Of course one can easily convert a TIFF stack for printing, but I found that the watershed algorithm for surface projections produces a more appealing result than just thresholding raw or deconvolved confocal data. One off-list message made the point that this could be a valuable tool for blind students and scientists. All the best, Tim Timothy Feinstein, Ph.D. | Manager, Core for Confocal Microscopy and Quantitative Imaging 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 Phone: 616-234-5819 | Email: [hidden email] On 1/7/15, 12:14 PM, "Mace, Emily Margaret" <[hidden email]> wrote: >***** >To join, leave or search the confocal microscopy listserv, go to: >http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >roscopy >Post images on >http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >posting. >***** > >Dear Tim, > >We have in fact done this on several scales using STED images surface >rendered in Huygens. We then pass them through Imaris to generate an STL >file and print them on a Makerbot. In the future it would be great to >have an STL file format option in Huygens (hint, hint). > >We are visualizing F-actin and, while it definitely generates great desk >art, there is also (as you put it) a non-zero analytical value of being >able to pick it up and look at it. In order to maximize this we are >playing with using dissolvable filament for the base and "filler", so we >can really see fine structure in 3D. We have put up one of our models on >the 3D print exchange here: >http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFT >hVW25aA&u=http%3a%2f%2f3dprint%2enih%2egov%2fdiscover%2f3dpx-000748 It's >broken into 4 components to keep the file size manageable. > >I'm happy to discuss details further if you like-- it's a fun exercise! > >Emily > > > >Emily Mace >Senior Postdoctoral Fellow, PhD >Laboratory of Jordan S. Orange, M.D., Ph.D. >Center for Human Immunobiology >Feigin Center >1102 Bates St >Baylor College of Medicine and Texas Children's Hospital >Houston, Texas, USA >Cell: 267-746-1843 >________________________________________ >From: Confocal Microscopy List <[hidden email]> on >behalf of Feinstein, Timothy <[hidden email]> >Sent: Wednesday, January 7, 2015 10:03 AM >To: [hidden email] >Subject: 3D printing > >***** >To join, leave or search the confocal microscopy listserv, go to: >http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >roscopy >Post images on >http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >posting. >***** > >Hello all, > >Has anyone tried exporting a surface rendering from Huygens, Imaris, >Volocity, Vaa3D etc for 3D printing? This is mostly a vanity exercise >for cool desk art, but aside from that I suspect that there is non-zero >analytical value in holding a structure in your hands. > >best, > > >Tim > >Timothy Feinstein, Ph.D. | Manager, Core for >Confocal Microscopy and Quantitative Imaging >333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 >Phone: 616-234-5819 | Email: >[hidden email]<mailto:[hidden email]> |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Tim, The 3D Viewer plugin in Fiji has options for stl export. I haven’t printed with it, only exporting to other software. There may be other plugins with vrml or stl exports that I haven’t tried yet. Regards, Glen MacDonald Core for Communication Research Virginia Merrill Bloedel Hearing Research Center Cellular Morphology Core Center on Human Development and Disability Box 357923 University of Washington Seattle, WA 98195-7923 USA (206) 616-4156 [hidden email] On Jan 7, 2015, at 2:57 PM, Feinstein, Timothy <[hidden email]> wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Thanks Emily! It turns out that Huygens does not support any export of > its surface rendering, at least not officially, but Imaris lets you export > its rendering as a VRML2 file. However at least in Imaris 7.4 you need to > manually edit the exported file extension from .vrml to .wrl before > software like Blender can open it and convert it to a .stl file for 3D > printing. I should note that Imaris is priced as a relatively niche > product and it would still be helpful to know if this can be done using > free software like Fiji or Vaa3d. > > Of course one can easily convert a TIFF stack for printing, but I found > that the watershed algorithm for surface projections produces a more > appealing result than just thresholding raw or deconvolved confocal data. > > One off-list message made the point that this could be a valuable tool for > blind students and scientists. > > All the best, > > > Tim > > Timothy Feinstein, Ph.D. | Manager, Core for > Confocal Microscopy and Quantitative Imaging > 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 > Phone: 616-234-5819 | Email: [hidden email] > > > > > > > > On 1/7/15, 12:14 PM, "Mace, Emily Margaret" <[hidden email]> wrote: > >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >> mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >> roscopy >> Post images on >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >> nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >> posting. >> ***** >> >> Dear Tim, >> >> We have in fact done this on several scales using STED images surface >> rendered in Huygens. We then pass them through Imaris to generate an STL >> file and print them on a Makerbot. In the future it would be great to >> have an STL file format option in Huygens (hint, hint). >> >> We are visualizing F-actin and, while it definitely generates great desk >> art, there is also (as you put it) a non-zero analytical value of being >> able to pick it up and look at it. In order to maximize this we are >> playing with using dissolvable filament for the base and "filler", so we >> can really see fine structure in 3D. We have put up one of our models on >> the 3D print exchange here: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFT >> hVW25aA&u=http%3a%2f%2f3dprint%2enih%2egov%2fdiscover%2f3dpx-000748 It's >> broken into 4 components to keep the file size manageable. >> >> I'm happy to discuss details further if you like-- it's a fun exercise! >> >> Emily >> >> >> >> Emily Mace >> Senior Postdoctoral Fellow, PhD >> Laboratory of Jordan S. Orange, M.D., Ph.D. >> Center for Human Immunobiology >> Feigin Center >> 1102 Bates St >> Baylor College of Medicine and Texas Children's Hospital >> Houston, Texas, USA >> Cell: 267-746-1843 >> ________________________________________ >> From: Confocal Microscopy List <[hidden email]> on >> behalf of Feinstein, Timothy <[hidden email]> >> Sent: Wednesday, January 7, 2015 10:03 AM >> To: [hidden email] >> Subject: 3D printing >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >> mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >> roscopy >> Post images on >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >> nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >> posting. >> ***** >> >> Hello all, >> >> Has anyone tried exporting a surface rendering from Huygens, Imaris, >> Volocity, Vaa3D etc for 3D printing? This is mostly a vanity exercise >> for cool desk art, but aside from that I suspect that there is non-zero >> analytical value in holding a structure in your hands. >> >> best, >> >> >> Tim >> >> Timothy Feinstein, Ph.D. | Manager, Core for >> Confocal Microscopy and Quantitative Imaging >> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 >> Phone: 616-234-5819 | Email: >> [hidden email]<mailto:[hidden email]> |
|
|
In reply to this post by Feinstein, Timothy
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Tim, I've converted tiff stacks to .stl files using the 3d viewer in Fiji. As long as the file isn't too big it seems to work. Doug > On Jan 7, 2015, at 5:57 PM, "Feinstein, Timothy" <[hidden email]> wrote: > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Thanks Emily! It turns out that Huygens does not support any export of > its surface rendering, at least not officially, but Imaris lets you export > its rendering as a VRML2 file. However at least in Imaris 7.4 you need to > manually edit the exported file extension from .vrml to .wrl before > software like Blender can open it and convert it to a .stl file for 3D > printing. I should note that Imaris is priced as a relatively niche > product and it would still be helpful to know if this can be done using > free software like Fiji or Vaa3d. > > Of course one can easily convert a TIFF stack for printing, but I found > that the watershed algorithm for surface projections produces a more > appealing result than just thresholding raw or deconvolved confocal data. > > One off-list message made the point that this could be a valuable tool for > blind students and scientists. > > All the best, > > > Tim > > Timothy Feinstein, Ph.D. | Manager, Core for > Confocal Microscopy and Quantitative Imaging > 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 > Phone: 616-234-5819 | Email: [hidden email] > > > > > > > >> On 1/7/15, 12:14 PM, "Mace, Emily Margaret" <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >> mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >> roscopy >> Post images on >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >> nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >> posting. >> ***** >> >> Dear Tim, >> >> We have in fact done this on several scales using STED images surface >> rendered in Huygens. We then pass them through Imaris to generate an STL >> file and print them on a Makerbot. In the future it would be great to >> have an STL file format option in Huygens (hint, hint). >> >> We are visualizing F-actin and, while it definitely generates great desk >> art, there is also (as you put it) a non-zero analytical value of being >> able to pick it up and look at it. In order to maximize this we are >> playing with using dissolvable filament for the base and "filler", so we >> can really see fine structure in 3D. We have put up one of our models on >> the 3D print exchange here: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFT >> hVW25aA&u=http%3a%2f%2f3dprint%2enih%2egov%2fdiscover%2f3dpx-000748 It's >> broken into 4 components to keep the file size manageable. >> >> I'm happy to discuss details further if you like-- it's a fun exercise! >> >> Emily >> >> >> >> Emily Mace >> Senior Postdoctoral Fellow, PhD >> Laboratory of Jordan S. Orange, M.D., Ph.D. >> Center for Human Immunobiology >> Feigin Center >> 1102 Bates St >> Baylor College of Medicine and Texas Children's Hospital >> Houston, Texas, USA >> Cell: 267-746-1843 >> ________________________________________ >> From: Confocal Microscopy List <[hidden email]> on >> behalf of Feinstein, Timothy <[hidden email]> >> Sent: Wednesday, January 7, 2015 10:03 AM >> To: [hidden email] >> Subject: 3D printing >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >> mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >> roscopy >> Post images on >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >> nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >> posting. >> ***** >> >> Hello all, >> >> Has anyone tried exporting a surface rendering from Huygens, Imaris, >> Volocity, Vaa3D etc for 3D printing? This is mostly a vanity exercise >> for cool desk art, but aside from that I suspect that there is non-zero >> analytical value in holding a structure in your hands. >> >> best, >> >> >> Tim >> >> Timothy Feinstein, Ph.D. | Manager, Core for >> Confocal Microscopy and Quantitative Imaging >> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 >> Phone: 616-234-5819 | Email: >> [hidden email]<mailto:[hidden email]> |
|
|
*****
To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi, after creating the stl file with either Fiji or Imaris) ( both works well), I had to simplify it using meshLab (http://www.shapeways.com/tutorials/polygon_reduction_with_meshlab) Indeed, if the 3d object is too complex , the software (like cura, makerware...) that prepares the code for the 3d-printing can freeze, or bug or ... Wish you all the best with your 3D printing, Romain --------------------------------------------------------------- Dr. Romain Guiet Bioimaging and Optics Platform (PT-BIOP) Ecole Polytechnique Fédérale de Lausanne (EPFL) Faculty of Life Sciences Station 19, AI 0140 CH-1015 Lausanne Phone: [+4121 69] 39629 http://biop.epfl.ch/ --------------------------------------------------------------- ________________________________________ De : Confocal Microscopy List [[hidden email]] de la part de Doug Richardson [[hidden email]] Envoyé : jeudi 8 janvier 2015 00:45 À : [hidden email] Objet : Re: 3D printing ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy Post images on http://www.imgur.com and include the link in your posting. ***** Hi Tim, I've converted tiff stacks to .stl files using the 3d viewer in Fiji. As long as the file isn't too big it seems to work. Doug > On Jan 7, 2015, at 5:57 PM, "Feinstein, Timothy" <[hidden email]> wrote: > > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > Post images on http://www.imgur.com and include the link in your posting. > ***** > > Thanks Emily! It turns out that Huygens does not support any export of > its surface rendering, at least not officially, but Imaris lets you export > its rendering as a VRML2 file. However at least in Imaris 7.4 you need to > manually edit the exported file extension from .vrml to .wrl before > software like Blender can open it and convert it to a .stl file for 3D > printing. I should note that Imaris is priced as a relatively niche > product and it would still be helpful to know if this can be done using > free software like Fiji or Vaa3d. > > Of course one can easily convert a TIFF stack for printing, but I found > that the watershed algorithm for surface projections produces a more > appealing result than just thresholding raw or deconvolved confocal data. > > One off-list message made the point that this could be a valuable tool for > blind students and scientists. > > All the best, > > > Tim > > Timothy Feinstein, Ph.D. | Manager, Core for > Confocal Microscopy and Quantitative Imaging > 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 > Phone: 616-234-5819 | Email: [hidden email] > > > > > > > >> On 1/7/15, 12:14 PM, "Mace, Emily Margaret" <[hidden email]> wrote: >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >> mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >> roscopy >> Post images on >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >> nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >> posting. >> ***** >> >> Dear Tim, >> >> We have in fact done this on several scales using STED images surface >> rendered in Huygens. We then pass them through Imaris to generate an STL >> file and print them on a Makerbot. In the future it would be great to >> have an STL file format option in Huygens (hint, hint). >> >> We are visualizing F-actin and, while it definitely generates great desk >> art, there is also (as you put it) a non-zero analytical value of being >> able to pick it up and look at it. In order to maximize this we are >> playing with using dissolvable filament for the base and "filler", so we >> can really see fine structure in 3D. We have put up one of our models on >> the 3D print exchange here: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFT >> hVW25aA&u=http%3a%2f%2f3dprint%2enih%2egov%2fdiscover%2f3dpx-000748 It's >> broken into 4 components to keep the file size manageable. >> >> I'm happy to discuss details further if you like-- it's a fun exercise! >> >> Emily >> >> >> >> Emily Mace >> Senior Postdoctoral Fellow, PhD >> Laboratory of Jordan S. Orange, M.D., Ph.D. >> Center for Human Immunobiology >> Feigin Center >> 1102 Bates St >> Baylor College of Medicine and Texas Children's Hospital >> Houston, Texas, USA >> Cell: 267-746-1843 >> ________________________________________ >> From: Confocal Microscopy List <[hidden email]> on >> behalf of Feinstein, Timothy <[hidden email]> >> Sent: Wednesday, January 7, 2015 10:03 AM >> To: [hidden email] >> Subject: 3D printing >> >> ***** >> To join, leave or search the confocal microscopy listserv, go to: >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqFv >> mUTS9MA&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic >> roscopy >> Post images on >> http://scanmail.trustwave.com/?c=129&d=g-2t1LM7LIzk04Ld9fknC-gPuY7l_qauqA7 >> nAz7pYA&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your >> posting. >> ***** >> >> Hello all, >> >> Has anyone tried exporting a surface rendering from Huygens, Imaris, >> Volocity, Vaa3D etc for 3D printing? This is mostly a vanity exercise >> for cool desk art, but aside from that I suspect that there is non-zero >> analytical value in holding a structure in your hands. >> >> best, >> >> >> Tim >> >> Timothy Feinstein, Ph.D. | Manager, Core for >> Confocal Microscopy and Quantitative Imaging >> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503 >> Phone: 616-234-5819 | Email: >> [hidden email]<mailto:[hidden email]> |
«
Return to Confocal Microscopy List
|
1 view|%1 views
| Free forum by Nabble | Edit this page |