Re: [MORPHMET] representing pointy structure using semilandmarks
Dear Karla Shikev, Have you tried digitising the tip of the pointy structure with a normal Landmark, and semi-landmarks before and after it to digitise the rest of the structure? This, of course, only works if the pointy structure is visible in all your specimens. Best wishes, Anneke van Heteren Op za 16 mrt. 2019 om 16:46 schreef Karla Shikev : > > Dear all, > > I've been trying to use sliding landmarks to represent the outlines of > different species and then to use those data to project the shapes onto a > morphospace (as in the Olsen et al. 2017). However, part of the outline > involves a local pointy structure that is functionally important, but that > simply disappears from the outlines of the morphospace. I tried to increase > the number of landmarks, but the problem remains. Any help would be greatly > appreciated. > > best, > > Karla > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > 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 --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] How to export .obj with textures as .ply with colours for morphometric analyses?
Dear Viviana If I remember correctly, you need to export, rather than save, your file to get a ply. I think there are some extra steps you need to take so that the ply doesn't come out colorless (something to do with the vertices I think), but like I said, I forgot the details and I don't have easy access to geomagic at the moment. Just keep fiddling with it. Good luck! All the best, Anneke On Sep 7, 2016 5:52 PM, "M. Viviana Toro Ibacache" < mtoroibaca...@odontologia.uchile.cl> wrote: Dear Anneke, Geomagic seems to read the three files and saves them to generate a .wrl (not .ply) file that has indeed colours, although they are not in the right place. But that is a good start. I assume there is a Geomagic setting to generate the file I am missing so I will keep on trying. Luckily in the lab I currently am there is Geomagic... a freware option for everyone would always be great! Thanks and best wishes, Viviana 2016-09-07 16:39 GMT+02:00 Anneke van Heteren <a.h.vanhete...@gmail.com>: > Dear Viviana, > > Have you tried geomagic? It has been a while since I last used this > program so I forgot the details, but it is capable of importing obj files > with textures and then exporting coloured ply files. Like I said, I forgot > the exact steps you would have to take, but I have done it before, so it is > certainly possible. > I hope that somewhat helps you. > > Best wishes, > > Anneke van Heteren > On Sep 2, 2016 2:54 PM, "Antonio Profico" <antonio.prof...@uniroma1.it> > wrote: > > Dear Viviana, > > you can export the 3D model from MeshLab as wrl format (export mesh as). > After, you can open and display the new mesh in Avizo (Display Open > Inventor Scene). In this way you can acquire the landmark in Avizo. > > Best, > Antonio > > > 2016-09-01 13:31 GMT+02:00 M. Viviana Toro Ibacache < > mtoroibaca...@odontologia.uchile.cl>: > >> Deal Morphometricians, >> >> I have .obj files with textures from three .jpg photos. I can load and >> see the textures very nicely in Meshlab, but I need the textures to be >> transformed into a coloured .ply file to do geometric morphometric analyses >> (the landmarks are represented in the textures). So far it has not worked >> doing it from Meshlab, so my questions are: >> >> - I know I can place landmarks in Meshlab using the .obj file, but when I >> do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is >> there a limit to files size in Meshlab? I would rather not to downsample >> the mesh to not lose anatomical details. >> >> - When using the Transfer Texture to Vertex Color function, the texture >> gets messed. It seems from web forums that Mshlab takes only one of the (in >> this case) three .jpg files to do the colouring of the .ply mesh. Does >> anybody know how to fix this? Another freeware software? >> >> - Is there any landmark acquisition software that loads .obj files with >> textures? So far, I have not been able to do it in Landmark Editor, Evan >> toolbox, Avizo, Morpho nor Geomorph. >> >> Any help is greatly appreciated. >> >> Best (y saludos), >> Viviana >> >> >> >> -- >> >> *Viviana Toro-Ibacache DDS MSc PhD* >> Profesora Asistente *(Assistant Professor)* >> Centro de Análisis Cuantitativo en Antropología Dental (CA2) >> Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas >> Facultad de Odontología Universidad de Chile >> >> Dirección: Sergio Livingstone Pohlhammer 943 >> *(address)* Independencia, Región Metropolitana >> Chile >> Email:mtoroibaca...@odontologia.uchile.cl >> Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/ >> www.cienciaymemoria.cl/staff.html >> >> -- >> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >> --- >> You received this message because you are subscribed to the Google Groups >> "MORPHMET" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to morphmet+unsubscr...@morphometrics.org. >> > > > > -- > __ > > Antonio Profico > PhD > Department of Environmental Biology – Dipartimento di Biologia Ambientale > SAPIENZA Università di Roma > > Lab. 06 4991 2690 > Mob. 3293440766 > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receivin
Re: [MORPHMET] How to export .obj with textures as .ply with colours for morphometric analyses?
Dear Viviana, Have you tried geomagic? It has been a while since I last used this program so I forgot the details, but it is capable of importing obj files with textures and then exporting coloured ply files. Like I said, I forgot the exact steps you would have to take, but I have done it before, so it is certainly possible. I hope that somewhat helps you. Best wishes, Anneke van Heteren On Sep 2, 2016 2:54 PM, "Antonio Profico" <antonio.prof...@uniroma1.it> wrote: Dear Viviana, you can export the 3D model from MeshLab as wrl format (export mesh as). After, you can open and display the new mesh in Avizo (Display Open Inventor Scene). In this way you can acquire the landmark in Avizo. Best, Antonio 2016-09-01 13:31 GMT+02:00 M. Viviana Toro Ibacache < mtoroibaca...@odontologia.uchile.cl>: > Deal Morphometricians, > > I have .obj files with textures from three .jpg photos. I can load and see > the textures very nicely in Meshlab, but I need the textures to be > transformed into a coloured .ply file to do geometric morphometric analyses > (the landmarks are represented in the textures). So far it has not worked > doing it from Meshlab, so my questions are: > > - I know I can place landmarks in Meshlab using the .obj file, but when I > do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is > there a limit to files size in Meshlab? I would rather not to downsample > the mesh to not lose anatomical details. > > - When using the Transfer Texture to Vertex Color function, the texture > gets messed. It seems from web forums that Mshlab takes only one of the (in > this case) three .jpg files to do the colouring of the .ply mesh. Does > anybody know how to fix this? Another freeware software? > > - Is there any landmark acquisition software that loads .obj files with > textures? So far, I have not been able to do it in Landmark Editor, Evan > toolbox, Avizo, Morpho nor Geomorph. > > Any help is greatly appreciated. > > Best (y saludos), > Viviana > > > > -- > > *Viviana Toro-Ibacache DDS MSc PhD* > Profesora Asistente *(Assistant Professor)* > Centro de Análisis Cuantitativo en Antropología Dental (CA2) > Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas > Facultad de Odontología Universidad de Chile > > Dirección: Sergio Livingstone Pohlhammer 943 > *(address)* Independencia, Región Metropolitana > Chile > Email:mtoroibaca...@odontologia.uchile.cl > Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/ > www.cienciaymemoria.cl/staff.html > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- __ Antonio Profico PhD Department of Environmental Biology – Dipartimento di Biologia Ambientale SAPIENZA Università di Roma Lab. 06 4991 2690 Mob. 3293440766 -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. 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 --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
Re: [MORPHMET] Questions regarding correction for allometry & evolutionary allometry
Dear Nicole In a recent paper of mine, I have also dealt with both allometry and phylogeny, in a different way than Prof. Dean suggests. You might want to have a look; it might give you some ideas. Here is the link: http://link.springer.com/article/10.1007%2Fs13127-015-0238-2. Let me know if you do not have access and I will send you a PDF. Best wishes, Anneke van Heteren 2016-02-02 19:26 GMT+11:00 Adams, Dean [EEOBS] <dcad...@iastate.edu>: > Nicole, > > > > There is no need to perform multiple residual-based analyses. If you wish > to obtain shape residuals where both the phylogeny and allometry (size) > have been taken into account, these are found as residuals from the PGLS > analysis: shape~size|phylogeny. > > > > However, a question then is what will these size/phylogeny shape residuals > be used to investigate? If the intention is to then evaluate these > relative to some other factor (say groups), then the correct approach is > just to perform a factorial PGLS analysis, where: shape~size+factor | > phylogeny (shape is a function of size and some other factor, given the > phylogeny). Additionally, if that factor describes groups, you may wish to > include the size:group interaction term. > > > > In fact, if that is indeed the case, it is advisable NOT to perform the > analysis in piecemeal fashion, where residuals from one regression are then > used in a subsequent linear model to test other effects. The reason is that > if there is some interaction between model effects (say, between size and > groups), then the residuals from the first regression are not correctly > capturing the observed patterns of variation. This is the multivariate > equivalent of the ANCOVA problem, and why an ANOVA on residuals from a > regression is not always the same as performing the ANCOVA analysis. The > best solution is to simply perform the factorial model, and account for > size while examining other effects. For this correct approach, one simply > requires software that allows one to perform factorial PGLS. Geomorph (and > as I recall, NTSYS) will allow uesrs to perform factorial PGLS. > > > > Hope this is helpful. > > > > Dean > > > > Dr. Dean C. Adams > > Professor > > Department of Ecology, Evolution, and Organismal Biology > >Department of Statistics > > Iowa State University > > www.public.iastate.edu/~dcadams/ > > phone: 515-294-3834 > > > > *From:* Nicole Dzenowski [mailto:ndzenow...@gmail.com] > *Sent:* Monday, February 1, 2016 9:18 PM > *To:* MORPHMET <morphmet@morphometrics.org> > *Subject:* [MORPHMET] Questions regarding correction for allometry & > evolutionary allometry > > > > > Hi everyone, > > > > I had some questions regarding allometry correction. I'll be working with > closely related specimens on a project where I think a moderate chunk of > the shape variation is due to allometric size differences. Should (or can) > I correct for both, as in, regress shape on size and take the residuals and > then use a phylogenetic comparative method on those residuals and the size > data and then do another multivariate regression and then use the residuals > from that final regression as my new shape variables? > > > > Any help or direction is greatly appreciated. > > > > Thanks! > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > 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 > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > 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 --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
[MORPHMET] Re: physignal in geomorph
Dear all Thank you very much to those who have replied to my question. It turned out that my data was a 2D matrix instead of a 3D array and that that was causing the problem. Best wishes, Anneke On Thursday, June 11, 2015 at 1:41:55 PM UTC+2, Anneke van Heteren wrote: Dear friends and colleagues I am trying to run physignal in geomorph (R), but I am running into a problem I do not understand. Here is the code I am using and the error message: physignal(ursid_phyl, Regr_res_av, iter=99) Error in match.names(clabs, names(xi)) : names do not match previous names However: name.check(ursid_phyl,Regr_res_av) [1] OK But: match(ursid_phyl,Regr_res_av) [1] NA NA NA NA match(Regr_res_av,ursid_phyl) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA This suggested to me that physignal might need the columns to carry the same names rather than the rows (as my phylogeny is list of 4 and I have 15 landmarks=45 variables), but when I transposed my data, I get a different error message: trans_regr_res_av -t(Regr_res_av) physignal(ursid_phyl, trans_regr_res_av, iter=99) Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) : Number of taxa in data matrix and tree are not not equal. I do not know what I could try next to calculate physignal. Any help would be appreciated. This is the phylogeny that I am using: (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3); Thanks in advance. Best wishes, Anneke van Heteren -- 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] physignal in geomorph
Dear friends and colleagues I am trying to run physignal in geomorph (R), but I am running into a problem I do not understand. Here is the code I am using and the error message: physignal(ursid_phyl, Regr_res_av, iter=99) Error in match.names(clabs, names(xi)) : names do not match previous names However: name.check(ursid_phyl,Regr_res_av) [1] OK But: match(ursid_phyl,Regr_res_av) [1] NA NA NA NA match(Regr_res_av,ursid_phyl) [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA [24] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA This suggested to me that physignal might need the columns to carry the same names rather than the rows (as my phylogeny is list of 4 and I have 15 landmarks=45 variables), but when I transposed my data, I get a different error message: trans_regr_res_av -t(Regr_res_av) physignal(ursid_phyl, trans_regr_res_av, iter=99) Error in physignal(ursid_phyl, trans_regr_res_av, iter = 99) : Number of taxa in data matrix and tree are not not equal. I do not know what I could try next to calculate physignal. Any help would be appreciated. This is the phylogeny that I am using: (Ame:21.8,(Tor:14.5,((Uam:5.7,(Uth:3.3,(Usp:1.2,(Uma:1.0,Uar:1.0):0.2):2.1):2.4):0.0,(Hma:1.0,Mur:1.0):4.7):8.8):7.3); Thanks in advance. Best wishes, Anneke van Heteren -- 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]
English below! Beste vrienden en collega’s Dit emailadres houdt binnenkort op te bestaan en was de afgelopen paar weken al een tijdje onbereikbaar. Mocht u mij zonder success geprobeerd hebben te contacteren, probeert u het dan alstublieft nogmaals op anneke.vanhete...@uni-bonn.de. Gelieve dit emailadres ook te gebruiken voor toekomstige berichten. Bij voorbaat hartelijk dank. Met vriendelijke groeten, Anneke van Heteren Dear friends and colleagues This email address will soon cease to exist and was, in fact, already unavailable for some time during the past couple of weeks. In case you have tried to contact me during this period, please try again on anneke.vanhete...@uni-bonn.de. Please also use this email address for future correspondence. Thanking you in advance. Best wishes, Anneke van Heteren Darwinweg 2 - 2333 CR LeidenMeckenheimer Allee 176 - 53115 Bonn E anneke.vanhete...@naturalis.nlE anneke.vanhete...@uni-bonn.de anneke.vanhete...@naturalis.nl -- 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] Ontogenetic changes in morphology
Dear Adeline Yong Right now you are essentially plotting size (of the claw) against size (of the crab). What you are interested in is shape against size. I am not sure what program you are using now, but I would suggest MorphoJ, as it is quite user friendly. You should do a multivariate regression of the Procrustes coordinates onto size.You could then play around with different size measures. (ln) centroid size of the object of interest is commonly used for these types of analyses, but you could also try doing it with carapace size and see if you get different results. I hope that helps. Best wishes, Anneke van Heteren -- 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] Getting 3D landmarks and areas from 2D images
Dear Marc You could use photogrammetry to create 3D models, but it would require several photographs from different angles rather than just one from the top. I hope that helps. Best wishes, Anneke van Heteren Darwinweg 2 - 2333 CR LeidenMeckenheimer Allee 176 - 53115 Bonn E anneke.vanhete...@naturalis.nlE anneke.vanhete...@uni-bonn.de anneke.vanhete...@naturalis.nl anneke.vanhete...@naturalis.nl 2015-02-16 20:00 GMT+01:00 marcsrour marcsr...@gmail.com: Dear all, I have what might be either a very basic question or an impossible task. I am working on quantifying the area covered by epibionts on highly-curved oyster shells (500+ specimens). These have been photographed from the top, but the amount of curvature on some of them means that using 2D measurements is too unreliable. Is it possible to use these same images to get 3D areas? If not, is there any way to achieve a result photographically, without the need for surface scanning? Any help or ideas would be deeply appreciated,and apologies for the novice question! Marc -- 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.
