Re: [MORPHMET] Curve sliding semilandmarks

[Emma Sherratt]

Dear Lawrence,

You can use geomorph's gpagen function for sliding semilandmarks during
Procrustes superimposition, by minimising bending energy or by minimising
Procrustes distance.

I would say that it is better to sample the curve in IDAV Landmark
Editorwith many semilandmarks, in order to avoid as many issues of
smoothing the curve of interest. Also, if you link two or more curves
together in IDAV Landmark Editor, then first use digit.curves function in
geomorph to resample the semilandmarks of those curves (since IDAV Landmark
Editor does not consider two curves sharing 1 landmark as linked and places
equally distant semis on each curve separately).

Details of geomorph below in my signature, including the extensive help
guide.

Emma

~~~

Emma Sherratt, PhD.


Postdoctoral Researcher in the Keogh Lab

Division of Evolution, Ecology & Genetics
Research School of Biology
116 Daley Road
The Australian National University
Acton, ACT  2601
AUSTRALIA

email: emma.sherr...@gmail.com
office tel: +61 2612 54943
mob: +61 4234 19966
Twitter: @DrEmSherratt 
co-author of geomorph R package: Software website
 | CRAN website
 | googlegroups


Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
  `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians




On 7 December 2016 at 05:21, Lawrence Fatica 
wrote:

> Hi all,
>
> I am working on a project examining shape variation in the pelvis. I used
> IDAV Landmark to place four curves of five semilandmarks each (as well as
> several fixed landmarks) along the major contours of the pelvis. I plan on
> doing the analysis in R, but I am unsure what my options are for
> semilandmarks sliding along curves. I am particularly concerned that the
> semilandmarks will slide along their tangents and off the bone when using
> sliding protocols that do not include the 3D mesh itself.
>
> Is this something I should be worried about? Has anyone else had success
> using sliding semilandmarks along curves?
>
>
> Thanks in advance for any insight,
>
> Lawrence
>
> --
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Re: [MORPHMET] RE: micro-CT suggestions

[Murat Maga]

Dear Angelo,


I would stay 1172 as far  away possible as I can. It is  the $30 inkjet 
equivalent of the mCT world. Cheap to buy, very frustrating to operate. Also 
signal to noise (SNR) on that machines leaves much to be desired. They are also 
phasing it out (due to these constraints). Unless you are getting it a very 
good deal, hassles are usually not worth it. And if you ever decide to use 
contrast agents on your specimens, you would wish that you have gone with a 
higher energy equipment.


If you are into Bruker (skycan) line of products, there are  other excellent 
products to consider (e.g. 1275).


But as Tom emphasized below machine is only one part of it.


M






From: Thomas O'Mahoney 
Sent: Tuesday, December 6, 2016 1:03:58 PM
To: Angela Roggero; lk...@siue.edu
Cc: MORPHMET
Subject: Re: [MORPHMET] RE: micro-CT suggestions

Dera Luci and Angela Roggero,
Nikon and Northstar imaging are also manufacturers that are worth looking into. 
The Nikon XTH225 is extremely popular in the UK for digitising objects from 
~2cm up to ~50cm. Resolution varies between 3-5 microns and 100 microns, 
depending on sample size etc. If you are looking for high throughput of 
specimens below 10cm, a helical microCT such as the FEI heliscan (designed 
originally for scanning of rock core samples) or Scanco vivCT (designed for 
in-vivo scanning of rodents) may be worth looking at too.
As ever, remember that the machine is just the beginning! Factor in 
technicians, computing, file storage etc as well (this can add at least another 
$100k to a budget).
Best,
Tom


On 6 December 2016 at 08:10, Angela Roggero 
> wrote:

dear Luci,

we too are interested in buying a microCT, and are examining some instruments 
just now. Essentially, we want to scan hundreds of similar, small and 
low-density objects (insects), and recently tested both SkyScan 1174, and 1172 
(Brucker). Besides, I will be glad to know what is the better choice of microCT 
to be used on insects. Many thanks for any information, Angela Roggero

Il 06/12/2016 01.06, Murat Maga ha scritto:
Dear Luci,

The very short answer is, it depends on your application (scanning hundreds of 
same thing or a multi-user facility in which users will want to scan rocks, 
biological specimens, engine parts). The major companies I am familiar with are 
Bruker (Skyscan), Scanco and GE. Expect to pay anywhere from $250K to $700K, 
depending on the scanner you choose and your support agreement.

Whatever you choose, there are very good open source packages. If you are 
spending tens of thousands of dollars on your analysis and visualization 
software, you are wasting money.

M


From: Kohn, Luci [mailto:lk...@siue.edu]
Sent: Wednesday, November 30, 2016 6:41 AM
To: MORPHMET 
Subject: [MORPHMET] micro-CT suggestions


I am planning to apply for funding for a micro-CT unit (and associated 
software.  Does anyone have suggestions of models they would recommend?



Thanks in advance

Luci Kohn




Luci Kohn, Ph.D.
Associate Professor
Department of Biological Sciences, Box 1651
44 Circle Drive, SLW 1155
Southern Illinois University Edwardsville
Edwardsville, IL  62026-1651
Phone:  (618) 650-2394
Fax:  (618) 650-3174
e-mail:  lk...@siue.edu





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Dott. Angela Roggero
Dpt. Scienze della Vita e Biologia dei Sistemi
Via Accademia Albertina 13
I-10123 Torino - ITALY
Phone +39 011 670 4536
Fax +39 011 236 4536


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Re: [MORPHMET] micro-CT suggestions

[Joseph Kunkel]

Angela,

We are studying lobster cuticle with the SkyScan 1272 (which has a carousel 
sampler that holds 18 samples).  My regular sized object is a 6mm medallion of 
cuticle which can be scanned entirely at at 2.5 um resolution.  Smaller regions 
of interest can be analyzed but the size of the computational boundary must be 
smaller.  We recently published a MS on cuticle structures available at URL:  
http://www.bio.umass.edu/biology/kunkel/pub/reprints/FISH_4564_20161020JGKarch.pdf

We provide a Supplementar Table that lists the size of the scan and achievable 
resolution at that size.

The 1172 and 1174 both have a 6um resolution ‘limit’ perhaps associated with 
scanning larger structures.

I am not sure what the differentiates the 72 vs 74.   

-·.  .· ·.  .><º>·.  .· ·.  .><º>·.  .· ·.  .><º> .··.· >=-   
=º}><
Joseph G. Kunkel, Research Professor
112A Marine Science Center
University of New England
Biddeford ME 04005
http://www.bio.umass.edu/biology/kunkel/

> On Dec 6, 2016, at 3:10 AM, Angela Roggero  wrote:
> 
> dear Luci,
> we too are interested in buying a microCT, and are examining some instruments 
> just now. Essentially, we want to scan hundreds of similar, small and 
> low-density objects (insects), and recently tested both SkyScan 1174, and 
> 1172 (Brucker). Besides, I will be glad to know what is the better choice of 
> microCT to be used on insects. Many thanks for any information, Angela Roggero
> 
> Il 06/12/2016 01.06, Murat Maga ha scritto:
>> Dear Luci,
>>  
>> The very short answer is, it depends on your application (scanning hundreds 
>> of same thing or a multi-user facility in which users will want to scan 
>> rocks, biological specimens, engine parts). The major companies I am 
>> familiar with are Bruker (Skyscan), Scanco and GE. Expect to pay anywhere 
>> from $250K to $700K, depending on the scanner you choose and your support 
>> agreement.
>>  
>> Whatever you choose, there are very good open source packages. If you are 
>> spending tens of thousands of dollars on your analysis and visualization 
>> software, you are wasting money.
>>  
>> M
>>  
>>  
>> From: Kohn, Luci [mailto:lk...@siue.edu] 
>> Sent: Wednesday, November 30, 2016 6:41 AM
>> To: MORPHMET 
>> Subject: [MORPHMET] micro-CT suggestions
>>  
>> I am planning to apply for funding for a micro-CT unit (and associated 
>> software.  Does anyone have suggestions of models they would recommend?
>>  
>> Thanks in advance
>> Luci Kohn
>>  
>>  
>> Luci Kohn, Ph.D.
>> Associate Professor
>> Department of Biological Sciences, Box 1651
>> 44 Circle Drive, SLW 1155
>> Southern Illinois University Edwardsville
>> Edwardsville, IL  62026-1651
>> Phone:  (618) 650-2394
>> Fax:  (618) 650-3174
>> e-mail:  lk...@siue.edu
>>  
>>  
>>  
>> -- 
>> 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 tomorphmet+unsubscr...@morphometrics.org.
>> -- 
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>> --- 
>> 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.
> 
> -- 
> Dott. Angela Roggero
> Dpt. Scienze della Vita e Biologia dei Sistemi
> Via Accademia Albertina 13
> I-10123 Torino - ITALY 
> Phone +39 011 670 4536
> Fax +39 011 236 4536
> 
> -- 
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> --- 
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Re: [MORPHMET] RE: micro-CT suggestions

[Thomas O'Mahoney]

Dera Luci and Angela Roggero,
Nikon and Northstar imaging are also manufacturers that are worth looking
into. The Nikon XTH225 is extremely popular in the UK for digitising
objects from ~2cm up to ~50cm. Resolution varies between 3-5 microns and
100 microns, depending on sample size etc. If you are looking for high
throughput of specimens below 10cm, a helical microCT such as the FEI
heliscan (designed originally for scanning of rock core samples) or
Scanco vivCT (designed for in-vivo scanning of rodents) may be worth
looking at too.
As ever, remember that the machine is just the beginning! Factor in
technicians, computing, file storage etc as well (this can add at least
another $100k to a budget).
Best,
Tom


On 6 December 2016 at 08:10, Angela Roggero  wrote:

> dear Luci,
>
> we too are interested in buying a microCT, and are examining some
> instruments just now. Essentially, we want to scan hundreds of similar,
> small and low-density objects (insects), and recently tested both SkyScan
> 1174, and 1172 (Brucker). Besides, I will be glad to know what is the
> better choice of microCT to be used on insects. Many thanks for any
> information, Angela Roggero
>
> Il 06/12/2016 01.06, Murat Maga ha scritto:
>
> Dear Luci,
>
>
>
> The very short answer is, it depends on your application (scanning
> hundreds of same thing or a multi-user facility in which users will want to
> scan rocks, biological specimens, engine parts). The major companies I am
> familiar with are Bruker (Skyscan), Scanco and GE. Expect to pay anywhere
> from $250K to $700K, depending on the scanner you choose and your support
> agreement.
>
>
>
> Whatever you choose, there are very good open source packages. If you are
> spending tens of thousands of dollars on your analysis and visualization
> software, you are wasting money.
>
>
>
> M
>
>
>
>
>
> *From:* Kohn, Luci [mailto:lk...@siue.edu ]
> *Sent:* Wednesday, November 30, 2016 6:41 AM
> *To:* MORPHMET  
> *Subject:* [MORPHMET] micro-CT suggestions
>
>
>
> I am planning to apply for funding for a micro-CT unit (and associated
> software.  Does anyone have suggestions of models they would recommend?
>
>
>
> Thanks in advance
>
> Luci Kohn
>
>
>
>
>
> Luci Kohn, Ph.D.
> Associate Professor
> Department of Biological Sciences, Box 1651
> 44 Circle Drive, SLW 1155
> Southern Illinois University Edwardsville
> Edwardsville, IL  62026-1651
> Phone:  (618) 650-2394
> Fax:  (618) 650-3174
> e-mail:  lk...@siue.edu
>
>
>
>
>
>
>
> --
> 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.
> --
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> ---
> 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.
>
>
> --
> Dott. Angela Roggero
> Dpt. Scienze della Vita e Biologia dei Sistemi
> Via Accademia Albertina 13
> I-10123 Torino - ITALY
> Phone +39 011 670 4536 <+39%20011%20670%204536>
> Fax +39 011 236 4536 <+39%20011%20236%204536>
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
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> "MORPHMET" group.
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>

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Re: [MORPHMET] Curve sliding semilandmarks

[Thomas O'Mahoney]

Dear Lawrence,
Stefan Schlager's excellent Morpho package for R has the option to slide
semilandmarks without the mesh. I have had some success with this myself,
but you can of course include your mesh with these protocols in either
Morpho or Geomorph (written by Dean Adams et al.).
Best,
Tom

On 6 December 2016 at 18:21, Lawrence Fatica 
wrote:

> Hi all,
>
> I am working on a project examining shape variation in the pelvis. I used
> IDAV Landmark to place four curves of five semilandmarks each (as well as
> several fixed landmarks) along the major contours of the pelvis. I plan on
> doing the analysis in R, but I am unsure what my options are for
> semilandmarks sliding along curves. I am particularly concerned that the
> semilandmarks will slide along their tangents and off the bone when using
> sliding protocols that do not include the 3D mesh itself.
>
> Is this something I should be worried about? Has anyone else had success
> using sliding semilandmarks along curves?
>
>
> Thanks in advance for any insight,
>
> Lawrence
>
> --
> 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
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>

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Re: [MORPHMET] RE: micro-CT suggestions

[Angela Roggero]

dear Luci,

we too are interested in buying a microCT, and are examining some 
instruments just now. Essentially, we want to scan hundreds of similar, 
small and low-density objects (insects), and recently tested both 
SkyScan 1174, and 1172 (Brucker). Besides, I will be glad to know what 
is the better choice of microCT to be used on insects. Many thanks for 
any information, Angela Roggero



Il 06/12/2016 01.06, Murat Maga ha scritto:


Dear Luci,

The very short answer is, it depends on your application (scanning 
hundreds of same thing or a multi-user facility in which users will 
want to scan rocks, biological specimens, engine parts). The major 
companies I am familiar with are Bruker (Skyscan), Scanco and GE. 
Expect to pay anywhere from $250K to $700K, depending on the scanner 
you choose and your support agreement.


Whatever you choose, there are very good open source packages. If you 
are spending tens of thousands of dollars on your analysis and 
visualization software, you are wasting money.


M

*From:*Kohn, Luci [mailto:lk...@siue.edu]
*Sent:* Wednesday, November 30, 2016 6:41 AM
*To:* MORPHMET 
*Subject:* [MORPHMET] micro-CT suggestions

I am planning to apply for funding for a micro-CT unit (and associated 
software.  Does anyone have suggestions of models they would recommend?


Thanks in advance

Luci Kohn

Luci Kohn, Ph.D.
Associate Professor
Department of Biological Sciences, Box 1651
44 Circle Drive, SLW 1155
Southern Illinois University Edwardsville
Edwardsville, IL  62026-1651
Phone:  (618) 650-2394
Fax:  (618) 650-3174
e-mail: lk...@siue.edu 

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--
Dott. Angela Roggero
Dpt. Scienze della Vita e Biologia dei Sistemi
Via Accademia Albertina 13
I-10123 Torino - ITALY
Phone +39 011 670 4536
Fax +39 011 236 4536

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[MORPHMET] Curve sliding semilandmarks

[Lawrence Fatica]

 

Hi all,

I am working on a project examining shape variation in the pelvis. I used 
IDAV Landmark to place four curves of five semilandmarks each (as well as 
several fixed landmarks) along the major contours of the pelvis. I plan on 
doing the analysis in R, but I am unsure what my options are for 
semilandmarks sliding along curves. I am particularly concerned that the 
semilandmarks will slide along their tangents and off the bone when using 
sliding protocols that do not include the 3D mesh itself.

Is this something I should be worried about? Has anyone else had success 
using sliding semilandmarks along curves?


Thanks in advance for any insight,

Lawrence

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[MORPHMET] problem fixed

[andrea cardini]

Thanks to Marko Djurakic for finding the problem with the geiger 
function, and to all others who answered with suggestions: the issue was 
that another package had a function with the same name.


Cheers


Andrea


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/

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Re: [MORPHMET] geiger rescale error

[marko.djurakic via MORPHMET]

Hi Andrea,
The code you provided works for me and I am using R 3.2.2, geiger 2.0.6 
and ape_4.0.


However, ensure that the gegier is loaded in the R environment or ensure 
that other packages with the same function name do not possibly 
interfere with geiger (see this post: 
http://stackoverflow.com/questions/5564564/r-2-functions-with-the-same-name-in-2-different-packages). 
What might happen here is that when you called rescale function, R used 
rescale function from some other (loaded) packages (from different 
namespaces...). Try to run the new R session and load just geiger (with 
dependencies) using library (geiger) command, check the rescale function 
by getAnywhere("rescale") command and if rescale is called from the 
geiger () you will likely get an expected 
output (without error).
There is a shorter way as well. Load geiger and just type 
geiger::rescale().


Marko

On 2016-12-06 10:19, andrea cardini wrote:

Dear All,

I've just tried the rescale function in geiger on my data and got an
error message. As I have no experience with it, I tried the first
example for this function in the help: same error message (see below).

Has anyone had similar issues? Probably I made some silly mistake.

Thanks in advance for your feedback.

Cheers


Andrea


geo <- get(data(geospiza))
ltrns <- rescale(geo$phy, "lambda")
plot(ltrns(0))
title("lambda: 0.0")

Error message:

Error in rescale(as.numeric(x, range = range, domain = domain, ...)) :
  (list) object cannot be coerced to type 'double'


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università
di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human
Biology, The University of Western Australia, 35 Stirling Highway,
Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

ESTIMATE YOUR GLOBAL FOOTPRINT:
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/


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Re: [MORPHMET] geiger rescale error

[Carmelo Fruciano]

Hi Andrea,
I have run the code you posted without problems.
In this moment, I'm using R 3.3.2 x64 on a Windows machine.
The geiger version I tried this on is geiger_2.0.6.
You might wanna try also posting the question on the list R-sig-phylo  
as a lot of people developing R packages for phylogenetic comparative  
approaches are subscribers there (and that's why I'm answering to you  
publicly).

Best,
Carmelo

andrea cardini  ha scritto:


Dear All,

I've just tried the rescale function in geiger on my data and got an  
error message. As I have no experience with it, I tried the first  
example for this function in the help: same error message (see below).


Has anyone had similar issues? Probably I made some silly mistake.

Thanks in advance for your feedback.

Cheers


Andrea


geo <- get(data(geospiza))
ltrns <- rescale(geo$phy, "lambda")
plot(ltrns(0))
title("lambda: 0.0")

Error message:

Error in rescale(as.numeric(x, range = range, domain = domain, ...)) :
  (list) object cannot be coerced to type 'double'


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche,  
Università di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena  
- Italy

tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human  
Biology, The University of Western Australia, 35 Stirling Highway,  
Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics:  
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


ESTIMATE YOUR GLOBAL FOOTPRINT:  
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/


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Carmelo Fruciano
Postdoctoral Fellow - Queensland University of Technology - Brisbane,  
Australia

Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/

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[MORPHMET] geiger rescale error

[andrea cardini]

Dear All,

I've just tried the rescale function in geiger on my data and got an 
error message. As I have no experience with it, I tried the first 
example for this function in the help: same error message (see below).


Has anyone had similar issues? Probably I made some silly mistake.

Thanks in advance for your feedback.

Cheers


Andrea


geo <- get(data(geospiza))
ltrns <- rescale(geo$phy, "lambda")
plot(ltrns(0))
title("lambda: 0.0")

Error message:

Error in rescale(as.numeric(x, range = range, domain = domain, ...)) :
  (list) object cannot be coerced to type 'double'


--

Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, 
The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, 
Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

ESTIMATE YOUR GLOBAL FOOTPRINT: 
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/

--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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