Re: [MORPHMET] digitizing very variable leaves
Not for fractal dimension but this can be done using user friendly free softwares just google it Il gio 15 mar 2018 15:17 Tina Klenovšek <tina.klenov...@um.si> ha scritto: > Thank you very much, Paolo. I hope both can be done in NTSYSpc, because > unfortunately I don't use R. > > Tina > > > > *From:* Paolo Piras [mailto:paolopir...@gmail.com] > *Sent:* Thursday, March 15, 2018 2:14 PM > *To:* Carmelo Fruciano > *Cc:* MORPHMET > *Subject:* Re: [MORPHMET] digitizing very variable leaves > > > > Hi Tina, > > if your colleagues are interested in the complexity of the leaves shapes > more than in shape itself, it could be useful to compute the fractal > dimension of the outlines of the leaves; it is very easy and it does not > inform you about shape differences but about the "complexity" of the > outlines that of course does not require landmark's digitization or > homology. Shape Analysis and Fractal Diimension can be performed jointly > (e.g. Fourier Analysis) in order to have a more complete picture of the > phenomenon. > > Ciao > > Paolo > > > > > > > > > > > > > > > > > > > > > > 2018-03-15 12:25 GMT+01:00 Carmelo Fruciano <c.fruci...@unict.it>: > > Hi Tina, > > The software Shape by Iwata & Ukai is an user friendly option for > performing elliptic Fourier analysis. > > https://academic.oup.com/jhered/article/93/5/384/2187412 > > http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/ > > Elliptic Fourier analysis is also implemented in NTSYSpc, which is also > user-friendly. > > You probably want to read a bit on the methodology to see if it fits what > you plan to do and its potential shortcomings. > > I hope this helps. > > Carmelo > > > > On 15/03/2018 12:14, 'Tina Klenovšek' via MORPHMET wrote: > > Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf, > > > > my dilemma occurred because some botanists (I work with mammal skulls) > have asked me to help them evaluate leaf variability of two tree species > from different localities. So, variability within and among individual > trees and species. > > > > In which user friendly program (like MorphoJ J) can I analyse outline > data and visualize variability? > > > > Thank you again, > > Tina > > > > *From:* Joanna Lenarczyk [mailto:j.kowal...@botany.pl > <j.kowal...@botany.pl>] > *Sent:* Thursday, March 15, 2018 10:21 AM > *To:* Tina Klenovšek > *Subject:* Re: [MORPHMET] digitizing very variable leaves > > > > Hello Tina, > > You can try a program which does not need landmarks: > > > > http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html > > > > I hope it will help you :) I have not tried it yet by myself, but it can > be useful when you cannot or do not want use landmarks :) > > Best, > > Joanna > > > > 2018-03-15 8:40 GMT+01:00 <f.james.ro...@stonybrook.edu>: > > One could do that computationally but I would worry about the homology it > might imply for such variable leaf shapes. You might try it and then check > to see if, for example, a lobe on one leaf might be 20% of the linear > distance around the outline but in another it might be 30% of the way > around. In such a case the lobe on one leaf would effectively be treated as > homologous to a location between lobes on another leaf. If so, does that > make biological sense for your study? If simple leaves were also included > the implied homology of a point along its outline to that of one of the > lobed leaves might be pretty arbitrary. Would be better if one knew > something about the development of these leaves (which I do not!) and used > that knowledge. > > > > An alternative would be to use outline methods to group shapes for the > purpose of say identification with little implication that groups need be > biologically meaningful. Sorry to be rather negative but I find highly > variable leaf shapes difficult to put in a simple standard framework. > Perhaps others will have better suggestions. > > > > > > F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution > > Research Professor, Anthropology > > Stony Brook University > > > > *From:* Tina Klenovšek <tina.klenov...@um.si> > *Sent:* Wednesday, March 14, 2018 12:28 AM > *To:* f.james.rohlf <f.james.ro...@stonybrook.edu> > *Cc:* morphmet@morphometrics.org > *Subject:* RE: [MORPHMET] digitizing very variable leaves > > > > Thanks to everyone who answered. > > > > Dear Dr. Rohlf, > > I assumed great variability would be a pr
Re: [MORPHMET] digitizing very variable leaves
Hi Tina, if your colleagues are interested in the complexity of the leaves shapes more than in shape itself, it could be useful to compute the fractal dimension of the outlines of the leaves; it is very easy and it does not inform you about shape differences but about the "complexity" of the outlines that of course does not require landmark's digitization or homology. Shape Analysis and Fractal Diimension can be performed jointly (e.g. Fourier Analysis) in order to have a more complete picture of the phenomenon. Ciao Paolo 2018-03-15 12:25 GMT+01:00 Carmelo Fruciano <c.fruci...@unict.it>: > Hi Tina, > > The software Shape by Iwata & Ukai is an user friendly option for > performing elliptic Fourier analysis. > > https://academic.oup.com/jhered/article/93/5/384/2187412 > > http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/ > > Elliptic Fourier analysis is also implemented in NTSYSpc, which is also > user-friendly. > > You probably want to read a bit on the methodology to see if it fits what > you plan to do and its potential shortcomings. > > I hope this helps. > > Carmelo > > > > On 15/03/2018 12:14, 'Tina Klenovšek' via MORPHMET wrote: > > Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf, > > > > my dilemma occurred because some botanists (I work with mammal skulls) > have asked me to help them evaluate leaf variability of two tree species > from different localities. So, variability within and among individual > trees and species. > > > > In which user friendly program (like MorphoJ J) can I analyse outline > data and visualize variability? > > > > Thank you again, > > Tina > > > > *From:* Joanna Lenarczyk [mailto:j.kowal...@botany.pl > <j.kowal...@botany.pl>] > *Sent:* Thursday, March 15, 2018 10:21 AM > *To:* Tina Klenovšek > *Subject:* Re: [MORPHMET] digitizing very variable leaves > > > > Hello Tina, > > You can try a program which does not need landmarks: > > > > http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html > > > > I hope it will help you :) I have not tried it yet by myself, but it can > be useful when you cannot or do not want use landmarks :) > > Best, > > Joanna > > > > 2018-03-15 8:40 GMT+01:00 <f.james.ro...@stonybrook.edu>: > > One could do that computationally but I would worry about the homology it > might imply for such variable leaf shapes. You might try it and then check > to see if, for example, a lobe on one leaf might be 20% of the linear > distance around the outline but in another it might be 30% of the way > around. In such a case the lobe on one leaf would effectively be treated as > homologous to a location between lobes on another leaf. If so, does that > make biological sense for your study? If simple leaves were also included > the implied homology of a point along its outline to that of one of the > lobed leaves might be pretty arbitrary. Would be better if one knew > something about the development of these leaves (which I do not!) and used > that knowledge. > > > > An alternative would be to use outline methods to group shapes for the > purpose of say identification with little implication that groups need be > biologically meaningful. Sorry to be rather negative but I find highly > variable leaf shapes difficult to put in a simple standard framework. > Perhaps others will have better suggestions. > > > > > > F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution > > Research Professor, Anthropology > > Stony Brook University > > > > *From:* Tina Klenovšek <tina.klenov...@um.si> > *Sent:* Wednesday, March 14, 2018 12:28 AM > *To:* f.james.rohlf <f.james.ro...@stonybrook.edu> > *Cc:* morphmet@morphometrics.org > *Subject:* RE: [MORPHMET] digitizing very variable leaves > > > > Thanks to everyone who answered. > > > > Dear Dr. Rohlf, > > I assumed great variability would be a problem. > > I was thinking the best way of digitizing would be to draw a curve on the > outline of each leaf (simple and lobed leaves). Resample curves by length > with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, > the leaf tip and base, would be fixed others could be defined as > semi-landmarks. Is this sensible? > > Alternatively, we could analyse simple and lobed leaves separately. > > Thank you a lot for your help. > > > > Tina > > > > > > *From:* f.james.rohlf [mailto:f.james.ro...@stonybrook.edu > <f.james.ro...@stonybrook.edu>] > *Sent:* Wednesday, March 14, 2018 3:59 AM > *To:* Tina Klenovšek > *Subjec
Re: [MORPHMET] digitizing very variable leaves
Hi Tina, The software Shape by Iwata & Ukai is an user friendly option for performing elliptic Fourier analysis. https://academic.oup.com/jhered/article/93/5/384/2187412 http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/ Elliptic Fourier analysis is also implemented in NTSYSpc, which is also user-friendly. You probably want to read a bit on the methodology to see if it fits what you plan to do and its potential shortcomings. I hope this helps. Carmelo On 15/03/2018 12:14, 'Tina Klenovšek' via MORPHMET wrote: Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf, my dilemma occurred because some botanists (I work with mammal skulls) have asked me to help them evaluate leaf variability of two tree species from different localities. So, variability within and among individual trees and species. In which user friendly program (like MorphoJ J) can I analyse outline data and visualize variability? Thank you again, Tina *From:*Joanna Lenarczyk [mailto:j.kowal...@botany.pl] *Sent:* Thursday, March 15, 2018 10:21 AM *To:* Tina Klenovšek *Subject:* Re: [MORPHMET] digitizing very variable leaves Hello Tina, You can try a program which does not need landmarks: http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html I hope it will help you :) I have not tried it yet by myself, but it can be useful when you cannot or do not want use landmarks :) Best, Joanna 2018-03-15 8:40 GMT+01:00 <f.james.ro...@stonybrook.edu <mailto:f.james.ro...@stonybrook.edu>>: One could do that computationally but I would worry about the homology it might imply for such variable leaf shapes. You might try it and then check to see if, for example, a lobe on one leaf might be 20% of the linear distance around the outline but in another it might be 30% of the way around. In such a case the lobe on one leaf would effectively be treated as homologous to a location between lobes on another leaf. If so, does that make biological sense for your study? If simple leaves were also included the implied homology of a point along its outline to that of one of the lobed leaves might be pretty arbitrary. Would be better if one knew something about the development of these leaves (which I do not!) and used that knowledge. An alternative would be to use outline methods to group shapes for the purpose of say identification with little implication that groups need be biologically meaningful. Sorry to be rather negative but I find highly variable leaf shapes difficult to put in a simple standard framework. Perhaps others will have better suggestions. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University *From:*Tina Klenovšek <tina.klenov...@um.si <mailto:tina.klenov...@um.si>> *Sent:* Wednesday, March 14, 2018 12:28 AM *To:* f.james.rohlf <f.james.ro...@stonybrook.edu <mailto:f.james.ro...@stonybrook.edu>> *Cc:* morphmet@morphometrics.org <mailto:morphmet@morphometrics.org> *Subject:* RE: [MORPHMET] digitizing very variable leaves Thanks to everyone who answered. Dear Dr. Rohlf, I assumed great variability would be a problem. I was thinking the best way of digitizing would be to draw a curve on the outline of each leaf (simple and lobed leaves). Resample curves by length with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf tip and base, would be fixed others could be defined as semi-landmarks. Is this sensible? Alternatively, we could analyse simple and lobed leaves separately. Thank you a lot for your help. Tina *From:*f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] *Sent:* Wednesday, March 14, 2018 3:59 AM *To:* Tina Klenovšek *Subject:* Re: [MORPHMET] digitizing very variable leaves An assumption of the usual GMM methods is that shape variation is "small". I think these leaves exceed this quite a bit! Another problem is landmarks. How to match leaves with and without lobes? __ F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University Original message From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org <mailto:morphmet@morphometrics.org>> Date: 3/12/18 10:56 AM (GMT-10:00) To: morphmet@morphometrics.org <mailto:morphmet@morphometrics.org> Subject: [MORPHMET] digitizing very variable leaves Hello everyone, we would like to digitize tree leaves that are very variable (from simple oval to strongly lobed on one tree). 1.)I am wondering if TpsDig can do some kind of automatic digitizing like the LeafAnalyser software: http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes a defined number of landmarks on the leaf outline... LeafAnalyser does not seem flexible or precise enough. Or I can’t use it properly. A
RE: [MORPHMET] digitizing very variable leaves
Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf, my dilemma occurred because some botanists (I work with mammal skulls) have asked me to help them evaluate leaf variability of two tree species from different localities. So, variability within and among individual trees and species. In which user friendly program (like MorphoJ ☺) can I analyse outline data and visualize variability? Thank you again, Tina From: Joanna Lenarczyk [mailto:j.kowal...@botany.pl] Sent: Thursday, March 15, 2018 10:21 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves Hello Tina, You can try a program which does not need landmarks: http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html I hope it will help you :) I have not tried it yet by myself, but it can be useful when you cannot or do not want use landmarks :) Best, Joanna 2018-03-15 8:40 GMT+01:00 <f.james.ro...@stonybrook.edu<mailto:f.james.ro...@stonybrook.edu>>: One could do that computationally but I would worry about the homology it might imply for such variable leaf shapes. You might try it and then check to see if, for example, a lobe on one leaf might be 20% of the linear distance around the outline but in another it might be 30% of the way around. In such a case the lobe on one leaf would effectively be treated as homologous to a location between lobes on another leaf. If so, does that make biological sense for your study? If simple leaves were also included the implied homology of a point along its outline to that of one of the lobed leaves might be pretty arbitrary. Would be better if one knew something about the development of these leaves (which I do not!) and used that knowledge. An alternative would be to use outline methods to group shapes for the purpose of say identification with little implication that groups need be biologically meaningful. Sorry to be rather negative but I find highly variable leaf shapes difficult to put in a simple standard framework. Perhaps others will have better suggestions. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Tina Klenovšek <tina.klenov...@um.si<mailto:tina.klenov...@um.si>> Sent: Wednesday, March 14, 2018 12:28 AM To: f.james.rohlf <f.james.ro...@stonybrook.edu<mailto:f.james.ro...@stonybrook.edu>> Cc: morphmet@morphometrics.org<mailto:morphmet@morphometrics.org> Subject: RE: [MORPHMET] digitizing very variable leaves Thanks to everyone who answered. Dear Dr. Rohlf, I assumed great variability would be a problem. I was thinking the best way of digitizing would be to draw a curve on the outline of each leaf (simple and lobed leaves). Resample curves by length with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf tip and base, would be fixed others could be defined as semi-landmarks. Is this sensible? Alternatively, we could analyse simple and lobed leaves separately. Thank you a lot for your help. Tina From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] Sent: Wednesday, March 14, 2018 3:59 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves An assumption of the usual GMM methods is that shape variation is "small". I think these leaves exceed this quite a bit! Another problem is landmarks. How to match leaves with and without lobes? __ F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University Original message From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org<mailto:morphmet@morphometrics.org>> Date: 3/12/18 10:56 AM (GMT-10:00) To: morphmet@morphometrics.org<mailto:morphmet@morphometrics.org> Subject: [MORPHMET] digitizing very variable leaves Hello everyone, we would like to digitize tree leaves that are very variable (from simple oval to strongly lobed on one tree). 1.)I am wondering if TpsDig can do some kind of automatic digitizing like the LeafAnalyser software: http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes a defined number of landmarks on the leaf outline... LeafAnalyser does not seem flexible or precise enough. Or I can’t use it properly. Any experience? 2.)Is it possible/sensible to put objects that are so differently shaped (photos attached) into the same group or is it better to analyse simple and lobed leaves separately? I apologize if similar questions have been already answered... Kind regards, Tina Napaka! Ime datoteke ni navedeno. doc. dr. Tina Klenovšek, koordinatorica doktorskega študijskega programa Ekološke znanosti Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160<https://maps.google.com/
RE: [MORPHMET] digitizing very variable leaves
One could do that computationally but I would worry about the homology it might imply for such variable leaf shapes. You might try it and then check to see if, for example, a lobe on one leaf might be 20% of the linear distance around the outline but in another it might be 30% of the way around. In such a case the lobe on one leaf would effectively be treated as homologous to a location between lobes on another leaf. If so, does that make biological sense for your study? If simple leaves were also included the implied homology of a point along its outline to that of one of the lobed leaves might be pretty arbitrary. Would be better if one knew something about the development of these leaves (which I do not!) and used that knowledge. An alternative would be to use outline methods to group shapes for the purpose of say identification with little implication that groups need be biologically meaningful. Sorry to be rather negative but I find highly variable leaf shapes difficult to put in a simple standard framework. Perhaps others will have better suggestions. F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution Research Professor, Anthropology Stony Brook University From: Tina Klenovšek <tina.klenov...@um.si> Sent: Wednesday, March 14, 2018 12:28 AM To: f.james.rohlf <f.james.ro...@stonybrook.edu> Cc: morphmet@morphometrics.org Subject: RE: [MORPHMET] digitizing very variable leaves Thanks to everyone who answered. Dear Dr. Rohlf, I assumed great variability would be a problem. I was thinking the best way of digitizing would be to draw a curve on the outline of each leaf (simple and lobed leaves). Resample curves by length with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf tip and base, would be fixed others could be defined as semi-landmarks. Is this sensible? Alternatively, we could analyse simple and lobed leaves separately. Thank you a lot for your help. Tina From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] Sent: Wednesday, March 14, 2018 3:59 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves An assumption of the usual GMM methods is that shape variation is "small". I think these leaves exceed this quite a bit! Another problem is landmarks. How to match leaves with and without lobes? __ F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University Original message From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org <mailto:morphmet@morphometrics.org> > Date: 3/12/18 10:56 AM (GMT-10:00) To: morphmet@morphometrics.org <mailto:morphmet@morphometrics.org> Subject: [MORPHMET] digitizing very variable leaves Hello everyone, we would like to digitize tree leaves that are very variable (from simple oval to strongly lobed on one tree). 1.)I am wondering if TpsDig can do some kind of automatic digitizing like the LeafAnalyser software: http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes a defined number of landmarks on the leaf outline... LeafAnalyser does not seem flexible or precise enough. Or I can’t use it properly. Any experience? 2.)Is it possible/sensible to put objects that are so differently shaped (photos attached) into the same group or is it better to analyse simple and lobed leaves separately? I apologize if similar questions have been already answered... Kind regards, Tina doc. dr. Tina Klenovšek, koordinatorica doktorskega študijskega programa Ekološke znanosti Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160, 2000 Maribor, Slovenija T: +386 41 808 366 E: <mailto:ime.prii...@um.si> tina.klenov...@um.si, <http://www.fnm.uni-mb.si> www.fnm.um.si -- 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] digitizing very variable leaves
Thanks to everyone who answered. Dear Dr. Rohlf, I assumed great variability would be a problem. I was thinking the best way of digitizing would be to draw a curve on the outline of each leaf (simple and lobed leaves). Resample curves by length with approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf tip and base, would be fixed others could be defined as semi-landmarks. Is this sensible? Alternatively, we could analyse simple and lobed leaves separately. Thank you a lot for your help. Tina From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu] Sent: Wednesday, March 14, 2018 3:59 AM To: Tina Klenovšek Subject: Re: [MORPHMET] digitizing very variable leaves An assumption of the usual GMM methods is that shape variation is "small". I think these leaves exceed this quite a bit! Another problem is landmarks. How to match leaves with and without lobes? __ F. James Rohlf, Distinguished Prof. Emeritus Dept. Anthropology and Ecology & Evolution Stonybrook University Original message From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org> Date: 3/12/18 10:56 AM (GMT-10:00) To: morphmet@morphometrics.org Subject: [MORPHMET] digitizing very variable leaves Hello everyone, we would like to digitize tree leaves that are very variable (from simple oval to strongly lobed on one tree). 1.)I am wondering if TpsDig can do some kind of automatic digitizing like the LeafAnalyser software: http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes a defined number of landmarks on the leaf outline... LeafAnalyser does not seem flexible or precise enough. Or I can’t use it properly. Any experience? 2.)Is it possible/sensible to put objects that are so differently shaped (photos attached) into the same group or is it better to analyse simple and lobed leaves separately? I apologize if similar questions have been already answered... Kind regards, Tina [cid:image002.jpg@01D3BA4C.D9433EA0] doc. dr. Tina Klenovšek, koordinatorica doktorskega študijskega programa Ekološke znanosti Univerza v Mariboru | University of Maribor Fakulteta za naravoslovje in matematiko Faculty of Natural Sciences and Mathematics Koroška cesta 160, 2000 Maribor, Slovenija T: +386 41 808 366 E: tina.klenov...@um.si<mailto:ime.prii...@um.si>, www.fnm.um.si<http://www.fnm.uni-mb.si> -- 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.
