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 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 > *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 > > > > > > > > > > > > *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/?q=Koro%C5%A1ka+cesta+160&entry=gmail&source=g>, > 2000 Maribor, Slovenija > > T: +386 41 808 366 <+386%2041%20808%20366> > > E: tina.klenov...@um.si <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. > > > > > > -- > > Joanna Lenarczyk > > > Zakład Fykologii > > Instytut Botaniki im. W. Szafera Polskiej Akademii Nauk > > ul. Lubicz 46, 31-512 Kraków > > tel. 12 42 41 876 > > > > Department of Phycology > > W. Szafer Institute of Botany, Polish Academy of Sciences > > Lubicz 46, PL-31-512 Cracow > > phone +48 12 42 41 876 > > > > e-mail: j.lenarc...@botany.pl > > -- > 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 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. 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