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. 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
E: tina.klenov...@um.si <mailto:ime.prii...@um.si>, www.fnm.um.si
<http://www.fnm.uni-mb.si>
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Joanna Lenarczyk
Zakład Fykologii
Instytut Botaniki im. W. Szafera Polskiej Akademii Nauk
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Department of Phycology
W. Szafer Institute of Botany, Polish Academy of Sciences
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