Re: [MORPHMET] Doubt about scalling photos

[Donald Swiderski]

Anderson,

I want to add another point the others have not yet mentioned.

One very simple explanation could be that you are seeing parallax effects,
although it is hard to be sure without knowing which group represents which
magnification or where the points are on the skull.  At a minimum, the
camera will see less of the surface if it is closer to the surface – see
(A) in the attached figure for an extreme example (the reason is when the
camera is closer to the object, a ray of light traveling to the camera
aperture will be tangent to the surface for points closer to the center of
the field of view).  For related reasons, relief features will look
different due to both the camera’s distance from the object (B). You can
also easily show that this effect will vary with the distance of the
feature from the center of the field of view.

For these reasons, it is important to photograph larger objects from a
proportionately greater distance.  It is also a good idea to have the
region centered in the field of view, although you will still have to
consider whether the changes in the position of a landmark is due to
displacement of that feature, change in its relative height, or both.

On Fri, Jan 12, 2018 at 2:04 AM, Anderson Feijo  wrote:

> Dear Dean and Sonja,
>
> Thank you for your suggestions. I am exploring all these potential bias
> before starting my study. I have learned a lot through all comments and
> literature suggestions. I deeply appreciated your help.
>
> Best,
>
> Anderson
>
> On Tue, Jan 9, 2018 at 3:30 AM, Adams, Dean [EEOBS] 
> wrote:
>
>> Anderson,
>>
>>
>>
>> I don’t think you appreciated the importance of the Murat’s comments on
>> your earlier post on this same topic.
>>
>>
>>
>> In theory, there is no problem combining objects digitized at different
>> magnifications, or even digitized by different researchers. However, before
>> doing so one must carefully investigate for possible systematic biases in
>> digitizing, so they may be reduced to the greatest extent possible. If
>> there is some consistent bias in how objects are digitized in one ‘group’
>> relative to the other, this will permeate into perceived differences in
>> shape that may not exist. A common example with older digitizing tablets
>> would be differences in digitizing due to the handedness of the person
>> digitizing. Right-handed and left-handed individuals hold the stylus
>> differently which can result in consistent perceived shape differences of
>> the same objects once digitized.
>>
>>
>>
>> Whether or not you have such an issue with your two magnifications is
>> unclear. However, it is impossible to evaluate this without additional
>> replication. Again, as Murat suggested, try digitizing each object multiple
>> times at each magnification. Then one could obtain estimates of the
>> variation in digitizing at the same magnification versus across
>> magnifications to begin to discern whether the between-magnification
>> variation is greater than one might expect. If it is, then one must dig
>> deeper to determine why.
>>
>>
>>
>> I would recommend sorting all of this out before embarking on your
>> empirical study. Otherwise, interpreting patterns in the final dataset
>> becomes challenging to say the least.
>>
>>
>> Best,
>>
>>
>>
>> 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 <(515)%20294-3834>
>>
>>
>>
>> *From:* Anderson Feijo [mailto:andefe...@gmail.com]
>> *Sent:* Friday, December 29, 2017 3:19 AM
>> *To:* MORPHMET 
>> *Subject:* [MORPHMET] Doubt about scalling photos
>>
>>
>>
>> Hi everyone,
>>
>>
>>
>> I am starting a new project using GM which I will work with groups with
>> different sizes (e.g., rodents and small carnivores). I would like to find
>> a way to use the whole dataset in the analyses, instead of perform set of
>> analyses for each sized group. So, I did a test using one skull and place
>> the camera in two different distances to the object (~15 cm and ~30 cm). My
>> expectation was after scaling (using tpsDig) I wouldn´t have any meaningful
>> difference. But I got two clear groups that were statistically different.
>> So, my question is how can I combine 2D landmarks based on photos taken
>> from different distances of the camera to the object. I have attached here
>> the tps file (10 copies of the same skull, five at ~15cm and five at
>> ~30cm). I would be very grateful for any suggestion.
>>
>>
>>
>> All the best and Happy 2018!
>>
>>
>>
>> Anderson
>>
>> --
>> 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 

Re: [MORPHMET] Doubt about scalling photos

[Anderson Feijo]

Dear Dean and Sonja,

Thank you for your suggestions. I am exploring all these potential bias
before starting my study. I have learned a lot through all comments and
literature suggestions. I deeply appreciated your help.

Best,

Anderson

On Tue, Jan 9, 2018 at 3:30 AM, Adams, Dean [EEOBS] 
wrote:

> Anderson,
>
>
>
> I don’t think you appreciated the importance of the Murat’s comments on
> your earlier post on this same topic.
>
>
>
> In theory, there is no problem combining objects digitized at different
> magnifications, or even digitized by different researchers. However, before
> doing so one must carefully investigate for possible systematic biases in
> digitizing, so they may be reduced to the greatest extent possible. If
> there is some consistent bias in how objects are digitized in one ‘group’
> relative to the other, this will permeate into perceived differences in
> shape that may not exist. A common example with older digitizing tablets
> would be differences in digitizing due to the handedness of the person
> digitizing. Right-handed and left-handed individuals hold the stylus
> differently which can result in consistent perceived shape differences of
> the same objects once digitized.
>
>
>
> Whether or not you have such an issue with your two magnifications is
> unclear. However, it is impossible to evaluate this without additional
> replication. Again, as Murat suggested, try digitizing each object multiple
> times at each magnification. Then one could obtain estimates of the
> variation in digitizing at the same magnification versus across
> magnifications to begin to discern whether the between-magnification
> variation is greater than one might expect. If it is, then one must dig
> deeper to determine why.
>
>
>
> I would recommend sorting all of this out before embarking on your
> empirical study. Otherwise, interpreting patterns in the final dataset
> becomes challenging to say the least.
>
>
> Best,
>
>
>
> 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 <(515)%20294-3834>
>
>
>
> *From:* Anderson Feijo [mailto:andefe...@gmail.com]
> *Sent:* Friday, December 29, 2017 3:19 AM
> *To:* MORPHMET 
> *Subject:* [MORPHMET] Doubt about scalling photos
>
>
>
> Hi everyone,
>
>
>
> I am starting a new project using GM which I will work with groups with
> different sizes (e.g., rodents and small carnivores). I would like to find
> a way to use the whole dataset in the analyses, instead of perform set of
> analyses for each sized group. So, I did a test using one skull and place
> the camera in two different distances to the object (~15 cm and ~30 cm). My
> expectation was after scaling (using tpsDig) I wouldn´t have any meaningful
> difference. But I got two clear groups that were statistically different.
> So, my question is how can I combine 2D landmarks based on photos taken
> from different distances of the camera to the object. I have attached here
> the tps file (10 copies of the same skull, five at ~15cm and five at
> ~30cm). I would be very grateful for any suggestion.
>
>
>
> All the best and Happy 2018!
>
>
>
> Anderson
>
> --
> 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.
>



-- 
_

Dr. Anderson Feijó

Key Laboratory of Zoological Systematics and Evolution
Institute of Zoology, Chinese Academy of Science
Beichen West Road, Chaoyang District, 100101
Beijing, China

Curriculum: *Lattes ; ResearchGate
*

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RE: [MORPHMET] Doubt about scalling photos

[Adams, Dean [EEOBS]]

Anderson,

I don’t think you appreciated the importance of the Murat’s comments on your 
earlier post on this same topic.

In theory, there is no problem combining objects digitized at different 
magnifications, or even digitized by different researchers. However, before 
doing so one must carefully investigate for possible systematic biases in 
digitizing, so they may be reduced to the greatest extent possible. If there is 
some consistent bias in how objects are digitized in one ‘group’ relative to 
the other, this will permeate into perceived differences in shape that may not 
exist. A common example with older digitizing tablets would be differences in 
digitizing due to the handedness of the person digitizing. Right-handed and 
left-handed individuals hold the stylus differently which can result in 
consistent perceived shape differences of the same objects once digitized.

Whether or not you have such an issue with your two magnifications is unclear. 
However, it is impossible to evaluate this without additional replication. 
Again, as Murat suggested, try digitizing each object multiple times at each 
magnification. Then one could obtain estimates of the variation in digitizing 
at the same magnification versus across magnifications to begin to discern 
whether the between-magnification variation is greater than one might expect. 
If it is, then one must dig deeper to determine why.

I would recommend sorting all of this out before embarking on your empirical 
study. Otherwise, interpreting patterns in the final dataset becomes 
challenging to say the least.

Best,

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: Anderson Feijo [mailto:andefe...@gmail.com]
Sent: Friday, December 29, 2017 3:19 AM
To: MORPHMET 
Subject: [MORPHMET] Doubt about scalling photos

Hi everyone,

I am starting a new project using GM which I will work with groups with 
different sizes (e.g., rodents and small carnivores). I would like to find a 
way to use the whole dataset in the analyses, instead of perform set of 
analyses for each sized group. So, I did a test using one skull and place the 
camera in two different distances to the object (~15 cm and ~30 cm). My 
expectation was after scaling (using tpsDig) I wouldn´t have any meaningful 
difference. But I got two clear groups that were statistically different. So, 
my question is how can I combine 2D landmarks based on photos taken from 
different distances of the camera to the object. I have attached here the tps 
file (10 copies of the same skull, five at ~15cm and five at ~30cm). I would be 
very grateful for any suggestion.

All the best and Happy 2018!

Anderson
--
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Re: [MORPHMET] Doubt about scalling photos

[Sonja Windhager]

Dear Anderson Feijo, 

I assume that the difference is not a matter of scaling (that could be 
addressed with the Procrustes superimposition), but one of optical distortions 
caused by the lens. 
This paper exemplifies this for different lenses: 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149313 

Likewise, to minimize optical distortions with a small focal length you would 
need to enlarge the distance more than sharpness allows. 
If you have the possibility to use a 3D Scanner or photogrammetry, you could 
then set the viewing setting to “infinity” instead of mimicking a rather short 
lens for digitization. 

Best wishes, 
Sonja Windhager
—
Dr. Sonja Windhager
Department of Anthropology, University of Vienna (Lecturer) and
Department of Theoretical Biology, University of Vienna (Postdoc)
Althanstrasse 14, 1090 Wien, Austria
http://homepage.univie.ac.at/sonja.windhager/ 

http://theoretical.univie.ac.at/people/windhager/ 






> On 29 Dec 2017, at 10:18, Anderson Feijo  wrote:
> 
> Hi everyone,
> 
> I am starting a new project using GM which I will work with groups with 
> different sizes (e.g., rodents and small carnivores). I would like to find a 
> way to use the whole dataset in the analyses, instead of perform set of 
> analyses for each sized group. So, I did a test using one skull and place the 
> camera in two different distances to the object (~15 cm and ~30 cm). My 
> expectation was after scaling (using tpsDig) I wouldn´t have any meaningful 
> difference. But I got two clear groups that were statistically different. So, 
> my question is how can I combine 2D landmarks based on photos taken from 
> different distances of the camera to the object. I have attached here the tps 
> file (10 copies of the same skull, five at ~15cm and five at ~30cm). I would 
> be very grateful for any suggestion.
> 
> All the best and Happy 2018!
> 
> Anderson
> 
> -- 
> 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
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