Re: [MORPHMET] Different types of 2D and 3D image when intepreting PCA, CVA and other analysis.

[Helmi Hadi]

Hi Blake,

Thanks for the feedback. Will contact you later as well.

Kind regards,
Helmi

On Thursday, January 17, 2019 at 1:25:45 AM UTC+8, Blake Dickson wrote:
>
> Hi Helmi,
>
> I would concur with Murat. There aren't any satisfying options for 3D 
> data. The 3D landmarks from one or more angles for each extremity is really 
> your only option for publications. As for your final question, yes you can 
> output LM 'warps' for CVA, regression, or pretty much any ordination you 
> want, but your options on software that can do it are limited. Stephan 
> Schlager's R packages are a good start as Murat already suggested and I'm 
> happy to help work through some approaches in R if you want to shoot me an 
> email.
>
> Cheers,
> -Blake
>
>
> Blake Dickson
> PhD Candidate
> Museum of Comparative Zoology
> Harvard University
> 26 Oxford Street
> Cambridge, MA 02138
>
>
> On Tue, 15 Jan 2019 at 21:28, Murat Maga > 
> wrote:
>
>> Dear Helmi,
>>
>>  
>>
>> Visualizing deformation for 3D shapes is somewhat difficult, especially 
>> if you are planning to put in a 2D medium like a paper. What you suggested 
>> are your basic options. You can choose to do deformation grids 
>> independently for each plane, that way it is a bit easier to see what’s 
>> going on, especially on paper. 
>>
>>  
>>
>> I personally like animations, that is morphing from one (or more) PC 
>> extreme to the other interactively as it brings out the full benefit of 3D. 
>> You can do the same with regression coefficients (or CVs) as well. If you 
>> still have access, those should be available in Landmark Editor as you 
>> suggest. 
>>
>>  
>>
>> We have a working prototype that we are hoping to release in the few 6-8 
>> weeks that will let you do a bit more than what you can do in Landmark 
>> editor, including GPA and PCA, visualizing landmark variability, and 
>> plotting. I attached a screenshot to give you an idea. You can stack 
>> multiple PCs to visualize simultaneously. 
>>
>>  
>>
>> If landmark editor doesn’t work for you and you really need something 
>> shoot me an e-mail (off the list), I will try to help you. If you are 
>> comfortable with R, you can also give a Stefan Schlager’s Morpho package a 
>> try as well. 
>>
>>  
>>
>> M
>>
>>  
>>
>> *From:* Helmi Hadi > 
>> *Sent:* Tuesday, January 15, 2019 5:30 PM
>> *To:* MORPHMET >
>> *Subject:* [MORPHMET] Different types of 2D and 3D image when 
>> intepreting PCA, CVA and other analysis.
>>
>>  
>>
>> Dear Morphometricians,
>>
>>  
>>
>> Which kind of graphical output would be better to place when interpreting 
>> data output? I've made an imaginary PC graph with imaginary shape for 2D 
>> analysis. Transformation grid/wireframe show almost the same thing, except 
>> that transformation grid shows the bending energy. Wireframe removes the 
>> bending energy, but in return you get a sort of view of the overall shape. 
>> Wouldn't it be better for visualization to just find the raw data point 
>> corresponding to the furthest ends of the PCs and just placing it there. 
>> Then you get the fine details (curves) of the shape as well which you 
>> cannot capture with landmarks, unless you are planning to fully landmark 
>> the object. Example here is in the Leaf morphology article by Cardini. 
>> <https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0025630.g004>
>>  
>> It shows all three leaf morphology visual representation side by side.
>>
>>  
>>
>> For 3D, it will be harder to just use wireframe/transformational grid. 
>> Then should I either:
>>
>> 1. find the raw data of the extremities of the PC1 vs PC2 graph and place 
>> it in the graph or
>>
>> 2. take a raw specimen near the midpoint 0,0 value (in PC1 vs PC2) and 
>> just use IDAV to morph it to whichever PC which is displayed? 
>>
>>  
>>
>> If the raw data output itself can be used, can it be used for CVA, or 
>> Regression analysis as well? You can easily display the labels in MorphoJ 
>> and identify which raw data it corresponds to and just place it there. 
>>
>>  
>>
>> Thanks
>>
>>  
>>
>> Helmi
>>
>> -- 
>> 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.
>

Re: [MORPHMET] Different types of 2D and 3D image when intepreting PCA, CVA and other analysis.

[Helmi Hadi]

Dear Murat,

Thanks for the reply. That software screenshot looks great. It will 
definitely save time if you can stack PC output, rather than doing 
individual outputs and editing in Photoshop. 

Have not tried R. So not an expert with that software.

Kind regards,

Helmi

On Wednesday, January 16, 2019 at 10:28:07 AM UTC+8, Murat Maga wrote:
>
> Dear Helmi,
>
>  
>
> Visualizing deformation for 3D shapes is somewhat difficult, especially if 
> you are planning to put in a 2D medium like a paper. What you suggested are 
> your basic options. You can choose to do deformation grids independently 
> for each plane, that way it is a bit easier to see what’s going on, 
> especially on paper. 
>
>  
>
> I personally like animations, that is morphing from one (or more) PC 
> extreme to the other interactively as it brings out the full benefit of 3D. 
> You can do the same with regression coefficients (or CVs) as well. If you 
> still have access, those should be available in Landmark Editor as you 
> suggest. 
>
>  
>
> We have a working prototype that we are hoping to release in the few 6-8 
> weeks that will let you do a bit more than what you can do in Landmark 
> editor, including GPA and PCA, visualizing landmark variability, and 
> plotting. I attached a screenshot to give you an idea. You can stack 
> multiple PCs to visualize simultaneously. 
>
>  
>
> If landmark editor doesn’t work for you and you really need something 
> shoot me an e-mail (off the list), I will try to help you. If you are 
> comfortable with R, you can also give a Stefan Schlager’s Morpho package a 
> try as well. 
>
>  
>
> M
>
>  
>
> *From:* Helmi Hadi > 
> *Sent:* Tuesday, January 15, 2019 5:30 PM
> *To:* MORPHMET >
> *Subject:* [MORPHMET] Different types of 2D and 3D image when intepreting 
> PCA, CVA and other analysis.
>
>  
>
> Dear Morphometricians,
>
>  
>
> Which kind of graphical output would be better to place when interpreting 
> data output? I've made an imaginary PC graph with imaginary shape for 2D 
> analysis. Transformation grid/wireframe show almost the same thing, except 
> that transformation grid shows the bending energy. Wireframe removes the 
> bending energy, but in return you get a sort of view of the overall shape. 
> Wouldn't it be better for visualization to just find the raw data point 
> corresponding to the furthest ends of the PCs and just placing it there. 
> Then you get the fine details (curves) of the shape as well which you 
> cannot capture with landmarks, unless you are planning to fully landmark 
> the object. Example here is in the Leaf morphology article by Cardini. 
> <https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0025630.g004>
>  
> It shows all three leaf morphology visual representation side by side.
>
>  
>
> For 3D, it will be harder to just use wireframe/transformational grid. 
> Then should I either:
>
> 1. find the raw data of the extremities of the PC1 vs PC2 graph and place 
> it in the graph or
>
> 2. take a raw specimen near the midpoint 0,0 value (in PC1 vs PC2) and 
> just use IDAV to morph it to whichever PC which is displayed? 
>
>  
>
> If the raw data output itself can be used, can it be used for CVA, or 
> Regression analysis as well? You can easily display the labels in MorphoJ 
> and identify which raw data it corresponds to and just place it there. 
>
>  
>
> Thanks
>
>  
>
> Helmi
>
> -- 
> 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+u...@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] Different types of 2D and 3D image when intepreting PCA, CVA and other analysis.

[Helmi Hadi]

Dear Morphometricians,

Which kind of graphical output would be better to place when interpreting 
data output? I've made an imaginary PC graph with imaginary shape for 2D 
analysis. Transformation grid/wireframe show almost the same thing, except 
that transformation grid shows the bending energy. Wireframe removes the 
bending energy, but in return you get a sort of view of the overall shape. 
Wouldn't it be better for visualization to just find the raw data point 
corresponding to the furthest ends of the PCs and just placing it there. 
Then you get the fine details (curves) of the shape as well which you 
cannot capture with landmarks, unless you are planning to fully landmark 
the object. Example here is in the Leaf morphology article by Cardini. 

 
It shows all three leaf morphology visual representation side by side.

For 3D, it will be harder to just use wireframe/transformational grid. Then 
should I either:
1. find the raw data of the extremities of the PC1 vs PC2 graph and place 
it in the graph or
2. take a raw specimen near the midpoint 0,0 value (in PC1 vs PC2) and just 
use IDAV to morph it to whichever PC which is displayed? 

If the raw data output itself can be used, can it be used for CVA, or 
Regression analysis as well? You can easily display the labels in MorphoJ 
and identify which raw data it corresponds to and just place it there. 

Thanks

Helmi

-- 
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] Recommended phylogeny software and tutorial which works with morphoj

[Helmi Hadi]

Thank you. 

-- 
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] Recommended phylogeny software and tutorial which works with morphoj

[Helmi Hadi]

Dear morphometricians,

I would like to know more about how to incorporate a phylogeny tree into
morphoj. I have seen that morphoj uses a nexus file for the phylogeny tree.
I have never used a phylogeny software, so I am unsure what kind of data is
needed in order to generate a tree.

Does anyone know where to find articles/user guide about a user friendly
software? I am using a Windows PC and do not have a mac/Linux machine.

Kind regards,
Helmi
School of Health Sciences,
Universiti Sains Malaysia

-- 
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] Digital morphology data survey: ethics on data generation & use

[Helmi Hadi]

Done the survey. Quite interesting questions.

Regards.
Helmi

On 28 Jul 2017 22:48, "Christy Anna Hipsley" 
wrote:

> Dear Morphmet Community,
>
> I kindly ask your help in completing a short survey on trends in digital
> morphology data generation and use as part of a perspectives piece on the
> “Ethics of data sharing in the age of digital imaging”, which I will
> present at this year’s BioSyst EU meeting in Gothenburg, Sweden (
> http://www.conferencemanager.se/BiosystEU2017/speakers-and-symposia.html).
>
> While many recommendations have been made on best practices in this field,
> we as a community are still far from a consensus on how our data should be
> managed, both on the side of the people generating it and the people
> requesting it.
>
> Your responses are anonymous, and I will post the results on Morphmet at
> the end of the survey. The questions are focused on 3D digital morphology
> data (CT, laser scanning, etc), but please feel free to answer if you also
> deal with 2D images.
>
> To reach the survey, go here: https://goo.gl/forms/igFKPc376kVn5eI13
>
> The site will remain active for the next 2 weeks, until Friday, 11 August.
>
> Almost every question has the option to enter text, so please give as much
> information and opinions as possible to help us represent your concerns!
>
> Thank you for your time,
> Christy Hipsley & Emma Sherratt
>
>
> --
> 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.

Re: [MORPHMET] Does a research sample need to be normally distributed (male/female ratio) for PCA?

[Helmi Hadi]

Thank you for the explanation James. So that is why the ellipse is 
migrating towards the species 3 even though it does not have male species.

Regards,
Helmi

On Sunday, May 28, 2017 at 11:01:30 AM UTC+8, K. James Soda wrote:
>
> Dear Dr. Hadi,
>
> I would just like to add one additional comment to your question about the 
> need for normal distributions in PCA.  Dr. Mitteroecker is (of course) 
> correct that PCA does not make any distributional assumptions, but you 
> mentioned in passing that confidence ellipses are being placed around the 
> points.  Confidence ellipses usually do assume that the data is 
> multivariate normal.  There are distribution-free methods for placing 
> confidence intervals, but my suspicion is that these intervals would not 
> usually have an elliptical appearance unless the data was in fact normally 
> distributed.  
>
> So to reiterate:  PCA, no distributional assumptions.  Confidence 
> ellipses, usually assume multivariate normal data.  
>
> Hope that comment is useful,
>
> James
>
> On Thu, May 25, 2017 at 4:58 AM, Helmi Hadi  > wrote:
>
>> Dear morphometricians, 
>>
>> Does a sample need to be normally distributed when conducting PCA in 
>> geometric morphometrics? Sometimes due to research constraints there are no 
>> samples of the opposite sex. Someone was asking me this question, and I do 
>> not have the answer. When I look at the data distribution, there is quite 
>> an imbalance male/female population. However, the classifiers male/female 
>> and species are there and you can sort of tell which group belongs to 
>> where. My only fear is that the confidence ellipse for the males are being 
>> "gravitated" towards the females for one species as that species does not 
>> have any male specimens. Attached are the file which I have recreated the 
>> dataset based on memory. 
>>
>> Is this kind of data acceptable or publishable? 
>>
>> My own personal question is based on the GMM results given in MorphoJ. 
>> The PC1/PC2 axes does not intersect at the middle (which I have personally 
>> drawn the dotted line there). I don't mind this output, but does it matter 
>> to have the axes cut at the 0 value? The data data distribution does not 
>> change with the change of axes lines. I noticed some GMM papers have the 
>> axes at 0. 
>>
>> Thanks all for the help,
>>
>> Helmi Hadi,
>> School of Health Scienes, 
>> Universiti Sains Malaysia
>>
>> -- 
>> 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+u...@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] Re: Does a research sample need to be normally distributed (male/female ratio) for PCA?

[Helmi Hadi]

Thank you for the explanation Dr Philipp.


On Thursday, May 25, 2017 at 10:16:06 PM UTC+8, mitt...@univie.ac.at wrote:
>
> As an exploratory technique, PCA makes no distributional assumptions; it 
> is used to explore the empirical distribution of the data. The sample does 
> not need to be balanced with regard to sex or other grouping variables, but 
> larger groups have a stronger effect on the PCA than smaller groups.
>
> The origin of the coordinate system is arbitrary. However, many software 
> packages center the data so that the origin (i.e. where the axes intersect) 
> equals the mean value. 
>
>
>
> Am Donnerstag, 25. Mai 2017 09:58:31 UTC+2 schrieb Helmi Hadi:
>>
>> Dear morphometricians, 
>>
>> Does a sample need to be normally distributed when conducting PCA in 
>> geometric morphometrics? Sometimes due to research constraints there are no 
>> samples of the opposite sex. Someone was asking me this question, and I do 
>> not have the answer. When I look at the data distribution, there is quite 
>> an imbalance male/female population. However, the classifiers male/female 
>> and species are there and you can sort of tell which group belongs to 
>> where. My only fear is that the confidence ellipse for the males are being 
>> "gravitated" towards the females for one species as that species does not 
>> have any male specimens. Attached are the file which I have recreated the 
>> dataset based on memory. 
>>
>> Is this kind of data acceptable or publishable? 
>>
>> My own personal question is based on the GMM results given in MorphoJ. 
>> The PC1/PC2 axes does not intersect at the middle (which I have personally 
>> drawn the dotted line there). I don't mind this output, but does it matter 
>> to have the axes cut at the 0 value? The data data distribution does not 
>> change with the change of axes lines. I noticed some GMM papers have the 
>> axes at 0. 
>>
>> Thanks all for the help,
>>
>> Helmi Hadi,
>> School of Health Scienes, 
>> Universiti Sains Malaysia
>>
>

-- 
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] Does a research sample need to be normally distributed (male/female ratio) for PCA?

[Helmi Hadi]

Dear morphometricians, 

Does a sample need to be normally distributed when conducting PCA in 
geometric morphometrics? Sometimes due to research constraints there are no 
samples of the opposite sex. Someone was asking me this question, and I do 
not have the answer. When I look at the data distribution, there is quite 
an imbalance male/female population. However, the classifiers male/female 
and species are there and you can sort of tell which group belongs to 
where. My only fear is that the confidence ellipse for the males are being 
"gravitated" towards the females for one species as that species does not 
have any male specimens. Attached are the file which I have recreated the 
dataset based on memory. 

Is this kind of data acceptable or publishable? 

My own personal question is based on the GMM results given in MorphoJ. The 
PC1/PC2 axes does not intersect at the middle (which I have personally 
drawn the dotted line there). I don't mind this output, but does it matter 
to have the axes cut at the 0 value? The data data distribution does not 
change with the change of axes lines. I noticed some GMM papers have the 
axes at 0. 

Thanks all for the help,

Helmi Hadi,
School of Health Scienes, 
Universiti Sains Malaysia

-- 
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] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

[Helmi Hadi]

Hi Hadas,

Thank you for the reply. The test has been conducted previously before 
finalising the landmark points for other users. I suspect the raw bone data 
itself is unsatisfactory. The .obj files generated from 
PACS>MITK>MeshLab>IDAVLandmark to have problems. 

Kind regards,
Helmi

On Tuesday, October 11, 2016 at 4:50:12 AM UTC+8, Hadas L. wrote:
>
> Hi,
>
> I would consider doing a short reliability test on five specimens for each 
> individual for the single point landmarks and the curves. This shouldn't 
> take long and will give you an idea as to whether the landmarks are 
> reliable or not. Ideally this should be done before adding the landmarks to 
> the data set.
>
> Sincerely,
> Hadas
>
> On Sun, Oct 9, 2016 at 5:56 AM, Helmi Hadi  > wrote:
>
>> Dear Morphometricians, 
>>
>> I have a weird problem and I was hoping someone could help me on this. 
>>
>> I have the same CT bone (n=400) with 14 landmarks (2 Single point and 12 
>> sliding) larndmarked in IDAV Landmark by three different individuals 
>> following a figure key table. Each individual landmarked 100+ different 
>> bones. The figure key table has the shape of the bone, with the landmark 
>> locations and the order of landmarking. All users were briefed by a single 
>> person (user1) on how to extract the bone and landmark. All three 
>> individuals were present throughout the entire procedure but the bone 
>> segmentation and landmarking process was conducted individually. 
>>
>> When I combine all the data, I noticed that PC1 and PC2 graph has two 
>> clusters. The effect is about 55% (as detailed in the eigenvalues below) 
>> After further checking the classifiers in MorphoJ, the source of the 
>> clustering is one person (user1) landmarked it is slightly differently 
>> compared to the other two. I have checked the outliers tab and no glaring 
>> outliers exists. As the sample size is big, the curve seem to be quite 
>> normal. 
>>
>> Eigenvalues  % Variance Cumulative %
>>   1. 0.01603351  55.674   55.674
>>   2. 0.00496222  17.230   72.904
>>   3. 0.00224594   7.799   80.703
>>   4. 0.00121085   4.204   84.907
>>   5. 0.00076858   2.669   87.576
>> ...
>>
>> How to interpret the results for this kind of data? Things which come to 
>> my mind are:
>>
>> 1. Maybe the bones for user1 are different compared to the other two 
>> users.
>> Or 
>> 2. User1 thinks the landmark location slightly different compared to 
>> others.
>> Or
>> 3. User2 and 3 could not locate the landmark locations of user1.
>> Or
>> 4. The landmarks selected are unreliable.
>>
>> Ideally I would need few other people relandmark the entire set, but it 
>> is not possible to do it now. Can anyone help shed some light on what is 
>> the probable cause? Thank you.
>>
>>
>> Kind regards,
>>
>> Helmi Hadi, PhD
>>  School of Health Sciences, Universiti Sains Malaysia,
>> 16150 Kubang Kerian, Kelantan, MALAYSIA
>>
>>
>> -- 
>> 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+u...@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.

Re: [MORPHMET] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

[Helmi Hadi]

Dear Carmelo,

Thank you. I will try to look at the at that method. Thank you also for 
giving the reference material. The landmarks chosen has been tested to be 
replicable based on prior testing before deploying to other users. The 
first person briefed and thought all the other users the landmarking 
procedure and the segmentation and cleaning of the bone in PACS (a CT 
database). I will have a look at raw ct files first and try to get it 
landmarked. Maybe some people see the semi-landmarks slightly differently. 

Kind regards,
Helmi 

On Monday, October 10, 2016 at 8:28:32 AM UTC+8, Carmelo Fruciano wrote:
>
> Dear Helmi, 
> I won't answer you in detail on your specific case as I didn't fully   
> understand the problem/design. 
>
> Ideally, if you have at least a subset of the same bones being   
> digitized by all the users/operators, you can check for your   
> hypothesis 1. 
>
> In some cases it might be possible to "remove" measurement error from   
> your data using the method presented in 
>
> Valentin AE, Penin X, Chanut JP, Sévigny JM, Rohlf FJ (2008) Arching 
> effect on fish body shape in geometric morphometric studies. Journal of 
> Fish 
> Biology 73:623–638. doi:10./j.1095-8649.2008.01961.x 
>
> That method and other approaches/issues are also discussed in my   
> recent review on the topic of measurement error 
>
> Fruciano C (2016) Measurement error in geometric morphometrics.   
> Development Genes and Evolution, 226(3):139–158. doi:   
> 10.1007/s00427-016-0537-4. 
>
> which might be useful to you to understand what's possible to do in   
> your specific case. 
>
> I hope this helps, 
> Carmelo 
>
>
>
>
>
> Helmi Hadi > ha scritto: 
>
> > Dear Morphometricians, 
> > 
> > I have a weird problem and I was hoping someone could help me on this. 
> > 
> > I have the same CT bone (n=400) with 14 landmarks (2 Single point and 12 
> > sliding) larndmarked in IDAV Landmark by three different individuals 
> > following a figure key table. Each individual landmarked 100+ different 
> > bones. The figure key table has the shape of the bone, with the landmark 
> > locations and the order of landmarking. All users were briefed by a 
> single 
> > person (user1) on how to extract the bone and landmark. All three 
> > individuals were present throughout the entire procedure but the bone 
> > segmentation and landmarking process was conducted individually. 
> > 
> > When I combine all the data, I noticed that PC1 and PC2 graph has two 
> > clusters. The effect is about 55% (as detailed in the eigenvalues below) 
> > After further checking the classifiers in MorphoJ, the source of the 
> > clustering is one person (user1) landmarked it is slightly differently 
> > compared to the other two. I have checked the outliers tab and no 
> glaring 
> > outliers exists. As the sample size is big, the curve seem to be quite 
> > normal. 
> > 
> > Eigenvalues  % Variance Cumulative % 
> >   1. 0.01603351  55.674   55.674 
> >   2. 0.00496222  17.230   72.904 
> >   3. 0.00224594   7.799   80.703 
> >   4. 0.00121085   4.204   84.907 
> >   5. 0.00076858   2.669   87.576 
> > ... 
> > 
> > How to interpret the results for this kind of data? Things which come to 
> my 
> > mind are: 
> > 
> > 1. Maybe the bones for user1 are different compared to the other two 
> users. 
> > Or 
> > 2. User1 thinks the landmark location slightly different compared to 
> others. 
> > Or 
> > 3. User2 and 3 could not locate the landmark locations of user1. 
> > Or 
> > 4. The landmarks selected are unreliable. 
> > 
> > Ideally I would need few other people relandmark the entire set, but it 
> is 
> > not possible to do it now. Can anyone help shed some light on what is 
> the 
> > probable cause? Thank you. 
> > 
> > 
> > Kind regards, 
> > 
> > Helmi Hadi, PhD 
> >  School of Health Sciences, Universiti Sains Malaysia, 
> > 16150 Kubang Kerian, Kelantan, MALAYSIA 
> > 
> > 
> > -- 
> > 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+u...@morphometrics.org . 
> > 
>
>
>
> -- 
> Carmelo Fruciano 
> Postdoctoral Fellow - Queensland University of Technology - Brisbane,   
> Australia 
> Honorary Fellow - University of Catania - Catania, Italy 
> e-mail c.fru...@unict.it  
> http://www.fruciano.it/research/ 
>
>

-- 
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] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

[Helmi Hadi]

Dear Morphometricians, 

I have a weird problem and I was hoping someone could help me on this. 

I have the same CT bone (n=400) with 14 landmarks (2 Single point and 12 
sliding) larndmarked in IDAV Landmark by three different individuals 
following a figure key table. Each individual landmarked 100+ different 
bones. The figure key table has the shape of the bone, with the landmark 
locations and the order of landmarking. All users were briefed by a single 
person (user1) on how to extract the bone and landmark. All three 
individuals were present throughout the entire procedure but the bone 
segmentation and landmarking process was conducted individually. 

When I combine all the data, I noticed that PC1 and PC2 graph has two 
clusters. The effect is about 55% (as detailed in the eigenvalues below) 
After further checking the classifiers in MorphoJ, the source of the 
clustering is one person (user1) landmarked it is slightly differently 
compared to the other two. I have checked the outliers tab and no glaring 
outliers exists. As the sample size is big, the curve seem to be quite 
normal. 

Eigenvalues  % Variance Cumulative %
  1. 0.01603351  55.674   55.674
  2. 0.00496222  17.230   72.904
  3. 0.00224594   7.799   80.703
  4. 0.00121085   4.204   84.907
  5. 0.00076858   2.669   87.576
...

How to interpret the results for this kind of data? Things which come to my 
mind are:

1. Maybe the bones for user1 are different compared to the other two users.
Or 
2. User1 thinks the landmark location slightly different compared to others.
Or
3. User2 and 3 could not locate the landmark locations of user1.
Or
4. The landmarks selected are unreliable.

Ideally I would need few other people relandmark the entire set, but it is 
not possible to do it now. Can anyone help shed some light on what is the 
probable cause? Thank you.


Kind regards,

Helmi Hadi, PhD
 School of Health Sciences, Universiti Sains Malaysia,
16150 Kubang Kerian, Kelantan, MALAYSIA


-- 
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] landmarking a translucent matching symmetry object (like flywings)

[Helmi Hadi]

Thank you for the answer Andrea. I have been doing that previously. It only 
just occurred to me now, if there are any differences in not doing it 
differently. 

Kind regards,
Helmi

On Thursday, July 28, 2016 at 4:11:58 PM UTC+8, alcardini wrote:
>
> Hi Helmi,
>
> other may have different views, but I would work on, say, the left wing 
> and the right one mirrored. Although those landmarks are likely to be very 
> precise, your 'eyes' might see left and right slightly differently, if one 
> is not mirrored, and you may introduce a small bias. This is of course 
> testable but I would not waste the time and simply mirror the images using 
> a batch command (available for instance in IRFANVIEW, which is free).
>
> Good luck.
>
> Cheers
>
>
> Andrea
>
> PS
>
> For the GPA, the mirroring won't matter if the software (MorphoJ and 
> Morphologika, for instance) can do it, but I would still worry about the 
> possible bias.
> On 28/07/16 09:59, Helmi Hadi wrote:
>
> Dear morphometricians, 
>
> I have an odd question. For a translucent matching symmetry object like 
> fly wings, the venation can be seen on both sides of the object. Should I 
> flip one side of the wing (left or right side) and landmark all wings in 
> one configuration or should I retain a sort of mirror image when 
> landmarking the object. Does it matter or will it affect analysis later on 
> say if I am classifying it based on side (if I add a left/right side 
> classifier)? 
>
> Thank you.
>
> Helmi Hadi,
> School of Health Sciences, 
> Universiti Sains Malaysia,
> Kelantan, Malaysia
>
>
> -- 
> 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+u...@morphometrics.org .
>
>
> -- 
>
> 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: alca...@gmail.com , andrea@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
>
>

-- 
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] landmarking a translucent matching symmetry object (like flywings)

[Helmi Hadi]

Dear morphometricians, 

I have an odd question. For a translucent matching symmetry object like fly 
wings, the venation can be seen on both sides of the object. Should I flip 
one side of the wing (left or right side) and landmark all wings in one 
configuration or should I retain a sort of mirror image when landmarking 
the object. Does it matter or will it affect analysis later on say if I am 
classifying it based on side (if I add a left/right side classifier)? 

Thank you.

Helmi Hadi,
School of Health Sciences, 
Universiti Sains Malaysia,
Kelantan, Malaysia


-- 
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] Re: Using Landmark software for generating 3D images

[Helmi Hadi]

 

Dear Luisa,

 

I have come across the problem before. I think the “out of memory” usage is 
due to the graphic card on the computer. Landmark works well with gaming 
graphic cards (Nvidia GeForce/AMD). Not graphic cards meant for CAD design 
(Nvidia Quadro/AMD Firepro). If you can source a laptop/desktop with a 
gaming graphic card, it may work. Also, Landmark works well with normal 
CPU’s (Intel/AMD)compared to server CPU’s (Xeon). 

 

Hope this helps.

 

Kind regards

 

Helmi Hadi, PhD

 

School of Health Sciences, Universiti Sains Malaysia,

16150 Kubang Kerian, Kelantan, MALAYSIA

Tel: +609 7677834; Fax:+609 7677515


On Tuesday, January 26, 2016 at 3:31:18 AM UTC+8, Luisa Pallares wrote:
>
> Hello everyone,
>
> I've been working with 3D morphometrics for a while, and finally I'm 
> moving to make 3D images of the 3D changes. Before I was using 2D 
> wireframes derived from 3D changes (using MorphoJ) - no so nice, I know.
>
> The first way to do this that I found is using the software Landmark. 
> However I'm having problems with the program performance. I'm using a 
> pretty potent computer ( Windows 7 ultimate (service pack 1)
> Processor Inter (R) Xeon (R) CPU E5-2643 @3.30GHz (2 processors), RAM 
> 64GB), but the program always shows a "out of memory" message when I try to 
> deform a surface (.ply) using landmark coordinates imported from MorphoJ 
> (.dta). 
>
> Anyone has had the same problem before? 
> Based on the system requirements listed in the Landmark documentation it 
> should be working nicely. 
>
> I'll appreciate very much if someone can give me a hand here.
> But, I will also appreciate information of how to make nice 3D shape 
> changes images with other software!
>
> Thanks,
>
> Luisa Pallares
>
> Department of Evolutionary Genetics 
> Max Planck Institute for Evolutionary Biology
> August-Thienemannstr. 2
> 24306 Plön, Germany
> Tel:04522 763 386pall...@evolbio.mpg.de 
>
>
>

-- 
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] Information on 3d portable scanner

[Helmi Hadi]

Dear all,

I too would like to know what are good 3D scanners. I have seen people use 
Microsoft Kinect for 3D scanning an object. Here is a video of it. 

https://www.youtube.com/watch?v=rQPTxiK-Crw

I think that 3D scanners will come down in price eventually. The Kinect is 
cheaper than commercial scanners though it is slightly of lower resolution. 

I noticed the Creaform  
(http://www.creaform3d.com/en/metrology-solutions/handheld-portable-3d-scanner-goscan-3d)
 and the Artek 3D scanner  
(http://www.artec3d.com/hardware/artec-spider#specifications) are almost 
similar in technology and resolution. Maybe it is better to get whichever is 
cheaper. 


Kind regards,
Helmi

School of Health Sciences, Universiti Sains Malaysia,
16150 Kubang Kerian, Kelantan, MALAYSIA
Tel: +609 7677834; Fax:+609 7677515




-Original Message-
From: morphmet [mailto:dsl...@morphometrics.org] 
Sent: 16 December 2015 03:24
To: Anna Loy ; Dennis E. Slice 
Cc: morphmet@morphometrics.org
Subject: Re: [MORPHMET] Information on 3d portable scanner

Replying to the list...

Hi, Anna! No, I am not familiar with that. For the grant that secured the HDI, 
we also included the purchase of the similar Artec hand scanner
(http://landing.artec3d.com/?keyword=artec%20scanner&gclid=CNHLk8TL3skCFUQ2gQod2YQMTQ)
for archaeological field work, but did not get enough money for both. 
For our lab, the table-top seemed the best choice. I have used (well, minions, 
you know...) the Artec hand scanner some years ago and it was a bit flaky, but 
worked. I understand now that folks are using it quite successfully. I wish we 
had one. I might can refer you to someone if no one on the list has info.

-ds

On 12/15/15 2:12 PM, Anna Loy wrote:
> Thank you Dennis!
>
> Do you have any info regarding the portables CREAFORM?
>
> Best
>
> Anna
> 
> Anna Loy
> Dip. Bioscienze e Territorio
> Università del Molise
> Contrada Fonte Lappone
> I-86090 Pesche (IS), Italy
> Tel. 0874 404100
> Cell. 3316265137
> mail: a@unimol.it 
>
>
>
>
> Il giorno 15/dic/2015, alle ore 19:31, Dennis E. Slice 
> mailto:dsl...@morphometrics.org>> ha scritto:
>
>> We have the HDI 109 scanner with automatic turntable. My minions tell 
>> me it is quite easy to use with ridiculous resolution (I no longer 
>> get to play with the toys. This is probably for the best.). Part of 
>> the proposal for this was to digitize mouse skulls, so we opted for 
>> higher resolution without color.
>>
>> We were recently asked to scan a human skull at full resolution. The 
>> resulting file was 10s of gigabytes. I believe bear skulls would be a 
>> challenge because of both physical and digital size. I suspect 
>> resolution is controllable. One student is currently looking at 
>> morphometrics-appropriate decimation algorithms.
>>
>> Attached are pics of a macaque we scanned rendering only the vertices.
>> The skull is about 100cm.
>>
>> Morpheus can't handle the full-res scan. Rendering done in Meshlab.
>> full resolution: 3.4 million vertices (only vertices shown)6.8 
>> million faces
>>
>> Morpheus
>> Pic 1) 500k vertices, 1000k faces
>> Pic 2) 50k vertices, 100k faces
>>
>> -ds
>>
>> On 12/13/15 2:54 PM, ANNA LOY wrote:
>>> Hello everyone
>>>
>>> Do any of you have experience with portable 3d scanner (no 
>>> structured
>>> light) like
>>>
>>> *CREAFORM HANDY SCAN700 AMETEK
>>> *http://www.creaform3d.com/en/metrology-solutions/portable-3d-scanne
>>> r-handyscan-3d
>>>
>>> *GOSCAN 3D CREAFORM*video demo
>>> https://www.youtube.com/watch?v=4IY1IN8swEc 2pounds no structured 
>>> light (no laser) molto veloce, res fino a 0.1 mm.
>>>
>>>
>>> They seems very fast and easy to use
>>>
>>> Also which are differences with portable structured light 3d 
>>> scanners like *HDI 120 Blue-Light Scanner 
>>> *?
>>>
>>> I should scan mammal skulls, from otters to bears, in various museum 
>>> collections
>>>
>>> Any advice or suggestions would be appreciated
>>>
>>> Thanks
>>>
>>> Anna
>>> ___
>>>
>>> Anna Loy
>>> Dip. Bioscienze e Territorio
>>> Università del Molise
>>> Contrada Fonte Lappone
>>> 86090 Pesche (IS), Italy
>>> e-mail istituzionale: a@unimol.it  
>>> 
>>> e-mail: anna.lo...@gmail.com  
>>> 
>>> Tel: +39 0874404140
>>> Fax: +39 087440123
>>> skype:anna.loy56
>>> http://scholar.google.com/citations?hl=it&user=_dVgP6YJ
>>> Project 'It is never too Darwin':
>>> Project therio.it  : 
>>> https://dibt.unimol.it/therio/ Assistan Editor Italian Journal of 
>>> Zoology
>>> http://www.tandfonline.com/toc/tizo20/current#.Uuv5YfjANf9
>>>
>>> --
>>> MORPHMET may be accessed via its webpage at 
>>> http://www.morphometrics.org
>>
>> --
>> If a response is important to you, keep trying -> I receive 50-100 
>> msgs/day
>>
>> --
>> MORPHMET may be accessed 

[MORPHMET] Re: Table-top 3D scanner recommendations

[Helmi Hadi]

Dear Dennis,

I have had demonstration session with the Artec MHT 
 (discontinued) from a research 
group in Spain. It is quite good with human faces. Able to scan dark faces 
(surfaces), glasses and facial hair as well. The person can open their eyes 
as well (if they don't mind constant LED flashes). However with hair and 
glasses, the glasses tend to "protrude" on the face. Scanning is quite 
quick. I think the portability of the Artec is a good feature as not all 
items can be placed on a rotating platform for scanning like the 
NextEngine. With the artec, you need to move around/have a rotating table 
or chair and scan it yourself. I assume the Spider is better than the MHT.

Another scanner is the Polhemus FastSCAN Cobra 
. I am not sure 
how this performs in relation to the Artec. I had use the Polhemus 
Scorpion. It is not as fast as the Artec, unable to scan dark. transluscent 
objects (without some sort of powder application). It is portable, but 
slightly bigger compared to the Artec. Metal objects are a problem with the 
Scorpion. 

If you do manage to find a scanner, would you mind sharing with us which 
model is best? Especially in the high-resolution and portable area. 

Kind regards,
Helmi

School of Health Sciences,
Universiti Sains Malaysia

On Tuesday, February 3, 2015 at 4:56:43 AM UTC+8, dslice wrote:
>
> Does anyone have any experience or recommendations for a high-resolution, 
> table-top 3D scanner?
>
> I am wanting to apply for a university equipment grant to get a scanner 
> for my lab (and anyone else who might need to scan). This will be in 
> collaboration with bio and archaeological and art researchers. These grants 
> usually run about $40kUSD.
>
> It seems the popular NextEngine scanner (~6000USD with all the extras) has 
> a resolution of approx. 0.1-0.3mm. That would be fine for my stuff - method 
> development and human-sized bones, but my bio colleagues deem that 
> inadequate for their needs - mouse-sized bones. We can get high-res from 
> microCT, but that takes forever - about a day per scan and the files are 
> huge, e.g., >30GB.
>
> Similarly, the Artec Spider (22,600USD) has a resolution of 0.1 mm. It 
> promises some advantages of hand-held scanning, which would benefit my 
> archaeological colleagues, but I am hearing from users it might not be so 
> great in actual usage. Not sure if it supports a turntable/table-top 
> operation option.
>
> So, does anyone have any suggestions?
> high-resolution
> portable (might need to travel with it)
> fast, easy table-top operation
> <$40kUSD
>
> -ds
>

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

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.

[MORPHMET] Motion tracking and GMM?

[Helmi Hadi]

Hi,

I was wondering if GMM analysis could be done on motion tracking subjects? 
Subjects in motion tracking usually wear metallic studs which appear on like 
stick figures on the computer. As GMM analyses points, will it not be easier to 
just use the points generated by the motion tracking studs? 

I can see a problem where the placement of the studs on the subject may not be 
accurate and registering the whole body may prove problematic. 

Thank you

Regards
Helmi Hadi
Universiti Sains Malaysia

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

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.