[MORPHMET] Warped Grids in MorphoJ
Hi All, I am running MorphoJ on Mac OSX. I am looking at morhological variation between two datasets. In each dataset, each specimen has four replicates. I combined the datasets, made classifier files and ran the Procrustes fit and generated the covariance matrix. How then do I make a vector diagram/warp grid that visualizes shape change between the average shape of the two datasets? Thanks in advance for your help. Mike Michael W. Holmes Ph.D. Candidate University of California, Berkeley Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California Berkeley, CA 94720 USA http://ib.berkeley.edu/labs/lacey/holmes2.html -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Warped Grids in MorphoJ
Dear Mike, One way you can do this is by using the canonical variates analysis function. Between two groups you will get the shape change graph associate with the difference between groups. Or you can go to Preliminaries average observations by... and choose the groups classifier, and then right click and disply graphs. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians On 13 February 2015 at 07:16, Michael Holmes mhol...@berkeley.edu wrote: Hi All, I am running MorphoJ on Mac OSX. I am looking at morhological variation between two datasets. In each dataset, each specimen has four replicates. I combined the datasets, made classifier files and ran the Procrustes fit and generated the covariance matrix. How then do I make a vector diagram/warp grid that visualizes shape change between the average shape of the two datasets? Thanks in advance for your help. Mike Michael W. Holmes Ph.D. Candidate University of California, Berkeley Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California Berkeley, CA 94720 USA http://ib.berkeley.edu/labs/lacey/holmes2.html -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Warped Grids in MorphoJ
Oh sorry, I think the latter way just shows the group mean from the overall mean - so you may need to do some cutting and pasting... Contact Chris Klingenberg, he might have an easier way up his sleeve. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians On 13 February 2015 at 09:02, Emma Sherratt emma.sherr...@gmail.com wrote: Dear Mike, One way you can do this is by using the canonical variates analysis function. Between two groups you will get the shape change graph associate with the difference between groups. Or you can go to Preliminaries average observations by... and choose the groups classifier, and then right click and disply graphs. Emma ~~~ Emma Sherratt, PhD. Lecturer in Zoology, Zoology Division, School of Environmental and Rural Science, Room L120 Bldg C02, University of New England, Armidale, NSW, Australia, 2351 Tel: +61 2 6773 5041 email: emma.sherr...@une.edu.au Caecilians are legless amphibians... * __ (\ .-. .-. /_) \\_//^\\_//^\\_// `` `` ``* learn more about them here: www.emmasherratt.com/caecilians On 13 February 2015 at 07:16, Michael Holmes mhol...@berkeley.edu wrote: Hi All, I am running MorphoJ on Mac OSX. I am looking at morhological variation between two datasets. In each dataset, each specimen has four replicates. I combined the datasets, made classifier files and ran the Procrustes fit and generated the covariance matrix. How then do I make a vector diagram/warp grid that visualizes shape change between the average shape of the two datasets? Thanks in advance for your help. Mike Michael W. Holmes Ph.D. Candidate University of California, Berkeley Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California Berkeley, CA 94720 USA http://ib.berkeley.edu/labs/lacey/holmes2.html -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] 3D images - manipulation and registration?
Hi Stefan, Thank you very much for the tip. The *pcAlign* function worked like a charm! Regards, Hildur On Thursday, February 5, 2015 at 3:45:56 PM UTC, Stefan Schlager wrote: Hi Hildur, you can try to use the function pcAlign (from my R-package Morpho), to align meshes by their PC-axes. And, if you like my (inofficial) package mesheR ( https://github.com/zarquon42b/mesheR) is sporting a variety of rigid, similarity, affine and elastic ICP registration procedures for 3D-meshes. Best Stefan On 04/02/15 14:22, Hildur Magnúsdóttir wrote: Hi everyone, I'm using geometric morphometrics to study variation in the shell morphology of the common whelk. I'm really interested in using 3D images as a basis for this study but I'm having problems with manipulation and registration (e.g. rigid registration) of my images prior to digitizing of landmarks. I'm using a MakerBot® Digitizer™ Desktop 3D Scanner for capturing the 3D images and it generates either .stl or .ply files that I read into the R for digitizing. My problem is that when I read those files into the R they are not all oriented in the same way inside the box in the rgl window, thus it is very hard to align them reliably so that the landmarks are truly comparable between individuals. So my question to you all is if you know of a method to align or register the 3D images before I read them into R? Or of a package in R that can perform this action? I would be very grateful for any advice on this, Hildur Hildur Magnúsdóttir PhD Student University of Iceland, Department of Life and Environmental Sciences and Hólar University College, Department of Aquaculture and Fish Biology Telephone: +354 823 2485 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+u...@morphometrics.org javascript:. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.