RE: [MORPHMET] Morphmet in the Future

2019-07-01 Thread Murat Maga
Dear Morphmet community,

Couple weeks prior to his sudden demise, I suggested Dennis to consider moving 
the morphmet at some point to a modern forum platform that support markups, 
code formatting and inline images.

You can check out https://discourse.slicer.org to see one in action. The main 
benefit that I see is the potential for a more community build up and 
engagement. For people who prefer to receive messages as emails (myself 
included), they can configure their accounts to subscribe to messages.

Discourse is open-source and free to install and to use on ones own servers.  
There are various hosted options for a small fee too, 
https://www.discourse.org/pricing.

It is sad having to talk about changes so soon after Dennis’s passing, but I 
thought it is an appropriate discussion to have.
M


From: K. James Soda 
Sent: Saturday, June 29, 2019 9:10 PM
To: MORPHMET 
Subject: [MORPHMET] Morphmet in the Future

Dear Fellow Morphometricians,

I want to give a quick comment about the future of morphmet after Dennis's 
passing so that any necessary changes will not come as a surprise. Please rest 
assure that it is not a question of whether morphmet will continue but rather 
if any different procedures will be required to make or view posts. Right now, 
morphmet is linked to morphometrics.org, which is a 
domain that belonged to Dennis himself. As a result, it is possible that, at 
some point in the future, morphmet may temporarily go down if the 
morphmetrics.org domain becomes unavailable.

What does this mean for you as a member? Right now, very little. You can 
continue to post to morphmet and new members can join morphmet without 
interruption. If in the future, this ceases to be the case, you will receive an 
invitation to a near identical Google group that will function in the same 
manner as morphmet has operated since the 2014 transition. Invitations will 
likely be distributed over the course of two to three days. The invitation 
email will include instructions on any changes to the submission process, which 
will likely only include a new email address for making posts and a new web 
address for the forum.

If you have any questions or concerns, please contact me either on or off of 
the list (k.jamess...@gmail.com).

Best regards,

James Soda


Interim Moderator
(Soon to be) Assistant Professor
Department of Mathematics
Quinnipiac University
Hamden, CT 06518

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RE: [MORPHMET] Help with surface scans

2019-04-23 Thread Murat Maga
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RE: [MORPHMET] Question about MorphoJ/Landmarking

2019-03-27 Thread Murat Maga
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A good place for you to start is the MorphoJ manual. Specifically the Preli=
minaries section
http://www.flywings.org.uk/MorphoJ_guide/frameset.htm?index.htm

As for how the selection of landmarks will affect the results, short answer=
 is it depends. We use landmarks to model a complex shape in a simple and r=
eproducible way. If your end goal is somehow dependent on having an accurat=
e estimate of variation (e.g 

[MORPHMET] 3D Morphometrics summer workshop application is online

2019-03-18 Thread Murat Maga
ontent-Type: multipart/alternative;
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Hi,

Please see the attached flyer for 3D morphometrics workshop we will be runn=
ing at the University of Washington Friday Harbor Lab from 08/25 thru 08/31=
, 2019. We are working on finalizing the program, which will be posted on t=
he website (https://SlicerMorph.github.io/2019_Summer_Workshop) in the next=
 two weeks.

Workshop is mixed-format and include topics such as theory of statistical s=
hape analysis, applied imaging, and high-throughput image analysis. Labs wi=
ll cover all aspects of conducting specimen-based research using 3D imaging=
. Practical topics (e.g., image processing and segmentation, visualization)=
 will be taught using the open-source 3D-Slicer visualization suite and the=
 SlicerMorph morphometrics toolkit (statistical shape analysis) Additional =
lab topics include using 3D specimen repositories to obtain data, tools and=
 methods for collaboration and reproducible research, introduction to data =
analysis through R/Python. Course material will be focused on volumetric (e=
.g., CT or microCT) 3D datasets, but will be equally applicable to data fro=
m 3D surface scanners.

There is no registration fee, and accommodation and meals are covered for t=
he selected participants thanks to generous support from NSF. Partial trave=
l support is also available for qualified candidates.

See the flyer for the application link and necessary documents. Application=
 deadline is May 1st

Please help us spread this notice.
Thanks,
M


A. Murat Maga, PhD
Assistant Professor
Division of Craniofacial Med.
Dept. of Pediatrics
University of Washington
&
Member
Center for Developmental Biology and Regenerative Med.
Seattle Children's Research Institute
https://SlicerMorph.github.io<https://slicermorph.github.io/>
Follow @SlicerMorph<http://twitter.com/intent/user?screen_name=3DSlicerMorp=
h>

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Hi,

Please see the attached flyer for 3D morphometrics w=
orkshop we will be running at the University of Washington Friday Harbor La=
b from 08/25 thru 08/31, 2019. We are working on finalizing the program, wh=
ich will be posted on the website
 (https://SlicerMorph.github.io/2019_Summer_Workshop;>https://Sl=
icerMorph.github.io/2019_Summer_Workshop) in the next two weeks.


Workshop is mixed-format and include topics such as =
theory of statistical shape analysis, applied imaging, and high-throughput =
image analysis. Labs will cover all aspects of conducting specimen-based re=
search using 3D imaging. Practical
 topics (e.g., image processing and segmentation, visualization) will be ta=
ught using the open-source 3D-Slicer visualization suite and the SlicerMorp=
h morphometrics toolkit (statistical shape analysis) Additional lab topics =
include using 3D specimen repositories
 to obtain data, tools and methods for collaboration and reproducible resea=
rch, introduction to data analysis through R/Python. Course material will b=
e focused on volumetric (e.g., CT or microCT) 3D datasets, but will be equa=
lly applicable to data from 3D surface
 scanners.

There is no registration fee, and accommodation and =
meals are covered for the 

[MORPHMET] Real-time 3D mesh deformations with SLicerMorph

2019-03-15 Thread Murat Maga
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Hello,

We have couple videos from the prototype of SlicerMorph:

https://www.youtube.com/watch?v=hMMR9GChek8 (Visualization of PCs in real-time 
using reference mesh landmark set)
https://www.youtube.com/watch?v=t8Dj3rOmt78 (feature to import data from 
specimen repositories, MorphoSource in this case)

We are waiting a few key changes to Slicer to settle down to release it as an 
extension. Namely, these are the new landmark annotation infrastructure, which 
will allow things like drawing free hands 3D open and closed curves, 3D angles, 
distances etc.
https://www.dropbox.com/s/ap67lmxo0xh77h0/OpenCurve.mkv?dl=0

Meanwhile, inputs are welcomed (please email me directly).
M


A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medicine
UW Dept. of Pediatrics
&
Member
Center for Developmental Biology and Regenerative Medicine
Seattle Children's Research Institute
https://SlicerMorph.github.io
Follow @SlicerMorph<https://twitter.com/SlicerMorph>

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Hello,

We have couple videos from the prototype of SlicerMo=
rph:

https://www.youtube.com/watch?v=3DhMMR9GC=
hek8">https://www.youtube.com/watch?v=3DhMMR9GChek8 (Visualization of P=
Cs in real-time using reference mesh landmark set)
https://www.youtube.com/watch?v=3Dt8Dj3rO=
mt78">https://www.youtube.com/watch?v=3Dt8Dj3rOmt78 (feature to import =
data from specimen repositories, MorphoSource in this case)

We are waiting a few key changes to Slicer to settle=
 down to release it as an extension. Namely, these are the new landmark ann=
otation infrastructure, which will allow things like drawing free hands 3D =
open and closed curves, 3D angles,
 distances etc. 
https://www.dropbox.com/s/ap67lmxo0xh77h0=
/OpenCurve.mkv?dl=3D0">https://www.dropbox.com/s/ap67lmxo0xh77h0/OpenCurve.=
mkv?dl=3D0

Meanwhile, inputs are welcomed (please email me dire=
ctly).
M


A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial 

RE: [MORPHMET] Centroid size

2019-02-28 Thread Murat Maga
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[MORPHMET] SlicerMorph pre-release demo and testing

2019-02-27 Thread Murat Maga
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Hi folks,

We are looking for people interested in testing our development version of =
SlicerMorph toolkit. As it stands, tools provided in SlicerMorph extension =
lets you:

  *   browse and download 3D specimens from specimen repositories like Morp=
hoSource.
  *   Utilize the existing functionality of the 3D Slicer to digitize landm=
arks from specimens, as well as taking 3D measurements of linear distances,=
 areas and volumes (last two would require segmentation).
  *   We provide a generalized Procrustes analysis to conduct Procrustes su=
perimposition of the landmarks, as well as visualization tools to study lan=
dmark variability, and the deformations associated with one (or more) PCs a=
s vectors or as in full 3D (a reference sample is required). Plotting of Pr=
ocrustes distances and PCs is also provided through the existing modules of=
 Slicer.
  *   Provides utility functions (e.g., convert IDAV landmark editor files =
to Slicer landmark, import reconstruction from Bruker/Skyscan microCTs as 3=
D volumes)

We are going to do an online demo of both 3D Slicer and SlicerMorph toolkit=
 on March 6th from 10-12pm (Pacific Standard Time) using webex. The first h=
our is going to be general Slicer functionality (Setting up Slicer, loading=
 3D volumes/models, 3D rendering, segmentation and 3D model creation, landm=
arking and measurements), and the second half will be specific to the Slice=
rMorph functionality. While you don't have to attend the demo to test our t=
oolkit, I think you will find it useful because we do piggy-back on existin=
g Slicer modules to accomplish specific tasks (e.g., plotting, control of 3=
D renderings etc).

There is an online signup form
https://forms.office.com/Pages/ResponsePage.aspx?id=3DW9229i_wGkSZoBYqxQYL0=
lnYz8n5LvRInWGoz5_LAC1UNlQxQ0pFVEJKRjVaS1cwS0JXMDFKTTY0NC4u

please provide your name and email, so that we can send you the Webex sessi=
on info and how to get the SlicerMorph and 3D Slicer package. The only requ=
est we have from attendees is to test the software on their own (we provide=
 sample data) after the demo and give us feedback and report issues through=
 an online survey. Depending on the interest and feedback, we might repeat =
these online sessions in future.

Note that if you are entirely new to landmark-based statistical shape analy=
sis and 3D morphology, this demo session might not be ideal for you, as it =
will cover a lot of ground in two hours. We are in process of finalizing th=
e contents of our intense summer workshop at UW Friday Harbor Lab (schedule=
d for Aug 25th to Sept 1st) which will be better suited for people starting=
 with 3D morphometrics. An announcement will be made for course registratio=
n and logistics in the next few weeks.

Feel free to pass this message people outside of morphmet.


A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medicine
UW Dept. of Pediatrics
&
Member
Center for Developmental Biology and Regenerative Medicine
Seattle Children's Research Institute
https://SlicerMorph.github.io
Follow @SlicerMorph<https://twitter.com/SlicerMorph>

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http://schemas.microsoft.com/o

[MORPHMET] data donation request

2018-12-19 Thread Murat Maga
7E61375124E7D83D4158A8BE0MWHPR08MB2894namp_
Content-Type: text/plain; charset="UTF-8"

Dear all,

I would like to renew my request for data donation for our morphometrics 
toolkit. We are particularly interested datasets that feature:


  *   Data from different type surface scanners
  *   Z stacks (from HREM, SPIM, Confocal, or plain old histology).
  *   Any kind of 3D data from non-vertebrates.

It will be great if the datasets can be accompanied with some annotated 
landmarks. Our data dropbox is located at
https://faculty.washington.edu/maga/data_dropbox/

If you encounter problems uploading your data (too big, etc), please contact me 
off the listserv and we will look for other options for data transfer.
Best wishes,


A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medicine
UW Dept. of Pediatrics
&
Member
Center for Developmental Biology and Regenerative Medicine
Seattle Children's Research Institute
https://SlicerMorph.github.io

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Re: [MORPHMET] Centroid size correlation with size

2018-11-18 Thread Murat Maga
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RE: [MORPHMET] Re: semilandmarks in biology

2018-11-11 Thread Murat Maga
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[MORPHMET] Looking for users of microCT other than Skyscan and Scanco

2018-10-19 Thread Murat Maga
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RE: [MORPHMET] Problem to export data from Landmak editor to MorphoJ

2018-10-10 Thread Murat Maga
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[MORPHMET] Data donation request

2018-09-04 Thread Murat Maga
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Dear all,

We (Seattle Children's, UW Friday Harbor Lab, and Duke) are recently funded=
 by NSF to develop an add-on package for the open-source 3D Slicer for an i=
ntegrated experience to retrieve, process, digitize (i.e., landmark) and vi=
sualize 3D biological specimens. We are just kicking off the project, and e=
xpecting the first prototype to be ready by Spring 2019. Part of the projec=
t is to help the community to get their data into open-source formats. Ther=
e is no specific systematic focus, as long as image data are 3D. From our r=
esearch, we are well endorsed with vertebrate CT, microCT and surface scans=
 from different scanner vendors, but are looking into sample data from dive=
rse set of organisms (and scales) to test our package. It will be greatly h=
elpful, if you can donate sample data for different organisms, and especial=
ly for 3D modalities apart from CT/microCT. There is a public data drop fol=
der located at:

https://faculty.washington.edu/maga/data_dropbox/

You will need to provide an e-mail address for us to get back in touch with=
 you, in case we have a question. Also please do provide a brief descriptio=
n of the dataset. If you have multiple files (e.g., image stacks, associate=
d landmarks, segmentations, etc.), please zip them as a single file. If you=
 send us any data in proprietary formats (Amira, Avizo, Geomagick, etc.), p=
lease provide us with a description of the format so that we can research w=
ays of converting them into an open format correctly and publish the workfl=
ow.

Feel free to forward this note to interested parties who may not be on morp=
hmet and thank you very much for your help!

M

A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medicine
UW Dept. of Pediatrics
&
Member
Center for Developmental Biology and Regenerative Medicine
Seattle Children's Research Institute

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Dear all,

We (Seattle Children's, UW Friday Harbor Lab, and Du=
ke) are recently funded by NSF to develop an add-on package for the open-so=
urce 3D Slicer for an integrated experience to retrieve, process, digitize =
(i.e., landmark) and visualize 3D
 biological specimens. We are just kicking off the project, and expecting t=
he first prototype to be ready by Spring 2019. Part of the project is to he=
lp the community to get their data into open-source formats. There is no sp=
ecific systematic focus, as long
 as image data are 3D. From our research, we are well endorsed with vertebr=
ate CT, microCT and surface scans from different scanner vendors, but are l=
ooking into sample data from diverse set of organisms (and scales) to test =
our package. It will be greatly
 helpful, if you can donate sample data for different organisms, and especi=
ally for 3D modalities apart from CT/microCT. There is a public data drop f=
older located at:

https://faculty.washington.edu/m

RE: [MORPHMET] Trouble with 2-D morphomeric analysis in geomorph

2018-08-02 Thread Murat Maga
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RE: [MORPHMET] How can I test the project for identification of unknown crania?

2018-04-02 Thread Murat Maga
We need to clarify a few things:

You already have 400 cases that you know the ancestry and sex, and you want to 
use this database to infer ancestry of two skulls, for which you already know 
the sex. All 400 cases, as well as your two unknown, specimens have associated 
landmark data that were landmarked in using identical protocols. Does that sum 
it up accurately?

If that’s the case, one solution would be to use derive a linear discriminant 
function, and see how well it accurately identifies your ‘known’ data. You can 
use all your landmark coordinates, your full (or partial) PCA results to derive 
the LDA. At this point your goal would be to validate the model. You have a 
large sample size and you can split half to derive the LD function, and the 
remaining to test the LD (i.e., treat them as unknowns). Once you a find a 
model and a parameter set that give you good predictions, than you can plug in 
your two samples, and get your results.

In my opinion this kind of analysis is simpler in R than any of the programs 
you mentioned below, since it requires frequent revising of the GPA fit (scale 
or not scale), use allometric regression (or not), use all derived coordinates 
(or not), etc… to get the best ‘tuned’ model for your existing data.

There are other ways than LD to do this, but the structure of the problem is 
more or less the same: Derive a model, test it, if it results in sensible 
predictions, then apply to your unknowns.

Hope this helps some…
M





From: Dr.Abdelnasser Ibrahim 
Sent: Monday, April 2, 2018 4:11 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] How can I test the project for identification of unknown 
crania?

Dear all,

I'm a Ph.D. student and I'm working with 3D CT scan geometric morphometric 
analysis for classification of known Malaysian crania to different sexes and 
ancestries.

I collected the landmarks using Stratovan software and did Principal component, 
canonical variate, procrustes ANOVA, and DF analysis using MorphoJ and SPSS. 
and did visualization using IDAV Landmark Editor software and did cluster 
analysis using PAST software and used SPSS for reliability tests.

I need to classify unknown crania. How can I test the project for 
identification of unknown crania?
I did CT scan for known 2 crania one male and another female and known 
ancestries. Then I collected the landmarks on the tested crania using the same 
protocol. Then I added the collected coordinates to the whole previously 
collected coordinates of 400 cases using Notepad ++ then run PCA and CVA on 
MorphoJ. then the tested crania were classified to the groups which already 
known from the archive before.
 Is this method true for testing the unknown case? or I need to use another 
method?

Regards,
Abdelnasser Ibrahim
Ph.D. student in Pathology department (Forensic Anthropology)
Hospital UKM, Cheras, Malaysia.
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[MORPHMET] 3D Quantitative Phenotyping Gateway (3DQPG): A Community Resource for Quantitative Phenotyping of Biological Structure

2018-03-15 Thread Murat Maga
Dear all,
I just learned that our resource allocation request on the NSF's XSEDE HPC 
infrastructure to create a science gateway for 3D quantitative phenotyping is 
approved. When implemented, this will be a cloud platform where registered 
users can upload their imaging datasets and use the provided R and associated 
mesh/image analysis on the virtual HPC cluster. In addition, we will also make 
the ANTs diffeomorphic deformable image registration library and its R package 
available on this gateway. Provided tools will enable generation of a 
population template from a set of volumetric images [1-2]. Average anatomical 
templates (or atlases) provide a least-biased coordinate system to study 
structure-function relationships [3]. They operate as a reference frame for 
understanding the variation in anatomy, and as a probabilistic space into which 
structural features are mapped. In more practical terms, templates can aid in 
the automated or semi-automated segmentation of complex morphology [4], or 
landmarking [5-6].  Our goals is to facilitate morphometric analysis of large 
structural datasets using open standards and analytical pipeline.
I expect the gateway in its rough form will be available by fall of this year. 
This year we have enough allocations to process about ~1000 medium resolution 
(i.e. 512^3 voxels or less) dataset. If you are interested, please get in touch 
with me at m...@uw.edu. I am particularly interested in 
hearing from developmental biologist or people working on model organisms.
M
[1] For volumetric dataset https://www.ncbi.nlm.nih.gov/pubmed/28656622
[2] For mesh based dataset https://www.ncbi.nlm.nih.gov/pubmed/29080945
[3] https://www.ncbi.nlm.nih.gov/pubmed/15501083
[4] https://www.ncbi.nlm.nih.gov/pubmed/24850858
[5] https://www.ncbi.nlm.nih.gov/pubmed/26628903
[6] https://www.ncbi.nlm.nih.gov/pubmed/26120349








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RE: [MORPHMET] Portable scanner for 3D models

2018-02-13 Thread Murat Maga
I would suggest microCT for things that small especially, if you can get access 
to one or have the specimens ship to an imaging facility.
Resolution (and detail) will be far superior, and the amount of work you will 
do to convert the voxel data to surface models is going to be far less than 
stitching 3-4 (or more) acquisition together to get a decent coverage.

M


From: Giada Giacomini [mailto:giada.giacomin...@gmail.com]
Sent: Tuesday, February 13, 2018 1:58 AM
To: CARLOS ALBERTO CARRION 
Cc: MORPHMET 
Subject: Re: [MORPHMET] Portable scanner for 3D models

Hello Carlos,

in my experience the only surface scanner which reconstructed in a decent way 
bat skulls is Breuckmann Laser Scan for small objects (model SmartSCAN R5/C5 
5.0). But I wouldn't consider it portable.
For Myotis species (in particular the small ones) you will need to take at 
least 3-4 acquisitions for each specimen and don't expect perfect results on 
teeth. But it's pretty good!!

If anyone has other suggestions on laser scans able to reconstruct bat skulls I 
would be very curious to know too.

Many thanks in advance

Giada

On Mon, Feb 12, 2018 at 5:00 PM, CARLOS ALBERTO CARRION 
> wrote:
Hi ,
I am looking forward to create 3D models of small bats skull ( genus Myotis). 
Anyone has a good insight on portable 3d scanner for this task

Thanks

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RE: [MORPHMET] DA value calculation

2018-01-07 Thread Murat Maga
Patrick,

You can calculate Procrustes distance between any two configuration using the 
procdist() function of the shapes package.
https://www.rdocumentation.org/packages/shapes/versions/1.2.3/topics/procdist

M


From: lv xiao [mailto:lxia...@gmail.com]
Sent: Saturday, January 06, 2018 5:37 PM
To: MORPHMET 
Subject: [MORPHMET] DA value calculation

Dear all,

Question 1: If I have a set of specimens which are object symmetry, how could I 
calculate directional asymmetry (DA) score for this set of specimen? I noted 
that after using bilat.symm function in geomorph, DA.component could be 
extracted, which contains two sets of coordinates. I guess DA score of the 
sample could be calculated from DA.component, can anyone show me the code 
necessary to derive DA score, whether in geomorph or any other software?

Question 2: A possibly related question is how (appreciated if R code is 
provided) to obtain the Procrustes distance between two specimens after GPA. I 
think I can calculate the Procrustes distance between the original and 
reflected and relabled mirrors for each specimen and averaging the Procrustes 
distance across all specimens to obtain DA score for my entire sample.

Question3: A third question which is unrelated to the previous two is that I 
noted that Procrustes Variance is used in Morphol.disparity function to compare 
morphological disparity across groups. Procrustes Variance is explained in the 
user manual as "the sum of the diagonal elements of the group covariance 
matrix." But where can I find some more detailed mathematical definition of 
Procrustes Variance?

Thank you very much for your help!

Best regards,
Patrick Wen
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RE: [MORPHMET] Issues with subsetting nts array with classifiers and plotTangentSpace visualization

2018-01-05 Thread Murat Maga
Skip,
As a work around you can subset your own data. All the values you will need to 
do your own PCA scatter plot is in the
pseudoxy.PCA$pcscores.

That way, you get to do choose the coloring scheme and symbols.


From: Phillip Skipwith [mailto:pskipw...@gmail.com]
Sent: Friday, January 5, 2018 2:00 PM
To: MORPHMET 
Subject: [MORPHMET] Issues with subsetting nts array with classifiers and 
plotTangentSpace visualization

Hi,

I'm using Geomorph to analyze a 3D landmark dataset. I'm having a number of 
issues both in subsetting my array and visualizing these data after Procrustes 
analysis. I'm working with a set of 28 specimens and 61 3D landmarks. Below is 
a sample of my .dta file from Landmark Editor.


trial.coords <- readland.nts('pseudoxy_project3.dta')

1 28L 183 0 Dim=3

C_infralineatus_AMNH165799
D_quadralineatus_AMNH153343
D_quadralineatus_AMNH153345
D_quadralineatus_AMNH160061
..
-9.8451595e+000  -2.8541670e+000  -2.8408973e+000
-1.0106355e+001  -5.0837624e-001  -1.3406076e+000
-8.7275896e+000  -2.4869413e+000  -1.2266474e+000
-7.3323584e+000  -3.362e+000  -3.0307722e+000
..

I then make classifiers for later grouping and subsetting based on species 
(please see below). I can neither subset the data or properly visualize the 
resulting PCA plot. I get can error regarding the class of my array dimnames.  
Instead of a PCA plot of the designated axes organized by species, I get two 3D 
plots of PC1 (positive and negative loadings) with no labeling or legend. Below 
is some of my simple code. I'm new to Geomorph, so any help or advice would be 
greatly appreciated. If need be, I can send a reduced dataset to help with 
troubleshooting.


pseudoxy.gpa <- gpagen(trial.coords, ProcD = TRUE, Proj = TRUE, print.progress 
= TRUE)

# PCA
categories.qpa <- strsplit(dimnames(pseudoxy.gpa$coords)[[3]], "_")
# unlist into matrix format
classifiers.qpa <- matrix(unlist(categories.qpa), ncol=3, byrow=T)
# add the specimen ID to the first column of the table
classifiers.qpa <- cbind(dimnames(pseudoxy.gpa$coords)[[3]], classifiers.qpa)
# rename the column headings
colnames(classifiers.qpa) <- c("FullID", "Genus", "Species", "ID")
# converts to data frame so can index using $
classifiers.qpa <- as.data.frame(classifiers.qpa)

gp <- as.factor(paste(classifiers.qpa$Genus, classifiers.qpa$Species)) # create 
grouping variable
sub.gpa <- coords.subset(A = pseudoxy.gpa$coords, group = gp)
# I get the following error
Error in dimnames(specimens)[[3]] <- names : 'dimnames' must be a list #trying 
to coerce dimnames to a list does not help

pseudoxy.PCA <- plotTangentSpace(pseudoxy.gpa$coords, groups = gp, label = 
TRUE, legend = TRUE, axis1 = 1, axis2 = 2, warpgrids = TRUE)

# See attachment for confusing plot.

Thanks in advance,

Skip


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RE: [MORPHMET] Doubt Scaling photos

2017-12-29 Thread Murat Maga
Dear Anderson,

It has nothing to do with the scale of your data (or least not directly).

As you can see, you actually performed those two digitization attempts 
differently. It is maybe 1-2 pixels off, but in a very consistent way (greens 
are from one scale, red is the other scale, and cross is the consensus shape). 
This type of systematic error commonly occur in digitization process, as one 
learns better or alters the way landmarks are digitized/defined along the 
process. In your case, perhaps higher resolution image gave a better definition 
(imaging sense) of landmarks, so you captured them very slightly differently 
than low-res image (but in a very consistent way).

If you are concerned, the first step perhaps is to do the same thing (i.e. 
digitization of same sample with different magnifications several times) with 
several real specimens and get a sense of the magnitude of this error in 
context of the biological variation. Then perhaps you can decide, whether you 
can actually combine digitization’s from different magnification levels. There 
is quite a bit of literature on this,  you can start with a recent review.

https://www.ncbi.nlm.nih.gov/pubmed/27038025

Is there a reason you are not using a single magnification level for all your 
samples?
M

[cid:image001.jpg@01D38100.CDDD1E80]

From: Anderson Feijo [mailto:andefe...@gmail.com]
Sent: Friday, December 29, 2017 1:35 AM
To: MORPHMET 
Subject: [MORPHMET] Doubt Scaling photos

Hi everyone,

I am starting a new project using GM working with groups with different sizes 
(eg. rodents and small carnivores). I would like to use the whole dataset 
combined in the analyses, instead of perform set of analyses for each sized 
group. So, I did a test using the same skull and place the camera in two 
distance to the object (~15 cm and ~30 cm). My expectation was after scaling 
(using tpsDig) I wouldn´t detect any meaningful difference in the dataset. 
However, I got two clear groups that were even statistically different. I have 
attached here the tps file that I used (10 copies of the same skull, 5 at ~15 
cm and 5 at ~30cm). My question is how can I combine two set of 2d landmarks 
based on photos taken from different distance to the object. I would greatly 
appreciate any suggestion.

All the Best and Happy 2018!

Anderson
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RE: [MORPHMET] Issue with digit.fixed on 3D mesh geomorph

2017-12-20 Thread Murat Maga
In my experience rgl tends to be slow with meshes with high number of vertices. 
You may want to do your data collection outside of R using programs optimized 
for handling high-resolution meshes, such as MeshLab or 3D Slicer, save your 
coordinates as a text file and import them into R.

M


From: Phillip Skipwith [mailto:pskipw...@gmail.com]
Sent: Friday, December 15, 2017 8:37 AM
To: MORPHMET 
Subject: [MORPHMET] Issue with digit.fixed on 3D mesh geomorph

Hi Everyone,

First: I apologize if this is a double posting.

I'm new to 3D geometric morphometrics, so this issue might turn out to be a 
trivial one with an easy fix. At the moment I'm trying to place landmarks on 
ply meshs (120 - 150k vertices) in geomorph using the digit.fixed function. 
However, when I set a landmark on a vertex of interest, the point does not 
attach to the correct spot. Rather, it vanishes somewhere deeper in the mesh. 
Increasing ptsize to something well above 3 helps a little, but not much. I 
realize that the help files use meshes below 30k vertices, but I lose a lot of 
information when I go that low. Has anyone else had this issue? Is it possible 
to select faces instead of vertices in geomorph (seems unlikely)?
I wondering if there was some special way of exporting ply files from Meshlab 
that I'm missing. At the moment I simplify my high resolution mesh with 
quadratic decimation, and then export the ASCII ply directly from Meshlab 
without fiddling with the settings. Is this right?

Any help would be greatly appreciated.

Best,

Skip
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[MORPHMET] Public high-resolution CT scans and genotype data

2017-09-29 Thread Murat Maga
Hi folks,

I had a chance to compile my published CT imaging, landmark and genotype data 
from last couple years into a project called 'Genetics of Craniofacial Shape in 
Mus' at the Open Science Framework. Project is publicly available at 
https://osf.io/w4wvg/

The bulk of the data comes from a mouse backcross between A/J (A) and C57BL/6J 
(B6) strains. There are about 500 head microCT scans and associated skull 
landmarks. Both of those can be readily visualized in 3D Slicer. The genotype 
(1449 SNPs) phenotype (sex, and litter) data is available as a R/qtl cross 
file. I hope to add the mandible landmarks when I have the chance, along with 
data from another paper, which is in review.

The repository also contains the microCT skull/mandible 'atlas' that was 
constructed using a large number of classical and wild-derived inbred Mus 
musculus strains, along with the code to conduct image processing and analysis 
in R.

Each project component has a wiki that explains  datasets with more detail. All 
data are provided freely. If you end up using data for a publication, please 
cite the project with its DOI and appropriate publication(s). Full-text 
publications (and citations) are available under the 'Zotero' section of the 
main project.

Hope you find it useful. Please let me know if you have questions, or encounter 
issues with the data.

Best wishes,
M







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RE: [MORPHMET] Question on Morpho

2017-07-14 Thread Murat Maga
Your values in csv are non-sensical.

I am not aware of a single function that will read the pts files, but you can 
loop over the list of files and use read.table to read any ascii format. So 
something like this would work for your case

pts.files=dir(patt='pts')
temp=read.table(file=pts.files[1], skip=2, sep=' ', header = F)
LM=array(dim=c(nrow(temp)), 3, length(pts.files))

for (i in 1:length) LM[,,i]=read.table(file=pts.files[i], skip=2, sep=" ", 
header=F)[,2:4]

I didn’t check it, so you may need to edit a few things.
M


From: Pablo Fisichella [mailto:fisichellapa...@gmail.com]
Sent: Friday, July 14, 2017 7:51 AM
To: Antonio Profico 
Cc: MORPHMET ; morphmet_modera...@morphometrics.org
Subject: Re: [MORPHMET] Question on Morpho

Dear Antonio

Excuse my delayed response. Thank you, your suggestion work quite fine, I made 
the GPA. However, as Paolo mentioned the coords looks so strange. I made .csv 
files from .pts files (in landmark). Here I attach one of my .csv and the 
corresponding .pts file. There is a way to read multiple .txt files from a 
folder similar to read.csv.folder?. which is the right format of the data 
frame? I have 3D coordinates derived from Amira and microscribe.

Thank you

2017-07-13 5:30 GMT-03:00 Antonio Profico 
>:
Dear Pablo,

try:  proc <- ProcGPA(a$arr).

The object "a" is a list, the array is an element (arr) of the list.

Let me know if works,

Antonio

2017-07-13 4:59 GMT+01:00 Pablo Fisichella 
>:
Dear All

I am using the package Morpho in order to make some GM analyses but I obtained 
some errors. Now I am trying to use the function read.csv.folder

I ran this command

a<-read.csv.folder("E:/Documents/Zan2", x = 2:44, y = 2:4, rownames = NULL, 
header = TRUE, dec = ",", sep = ";", pattern = "csv", addSpec = NULL, back = 
TRUE)

In the r console appeared my 5 files .csv (see below) with 43 
landmarks/semilandmark in 3 dimensions for 5 individuals (0093, 0137, 0377, 
1865, 1880)

Then I tried perform a Procrustes Analysis using this function: proc <- 
ProcGPA(a) however this error appear: Error in addo(a3) : please provide 3D 
numeric array

I feel that this error is related to my data array but I dont know how I can 
solve this in order to run a GPA

thanks in advance, I appreciate any help you can give me.

cheers,

Pablo

$arr
, , 0093

  X YZ
1  3.30e+08 -1.08e+08 5.22e+08
2  2.94e+08 -5.35e+07 5.12e+08
3  2.76e+08 -7.79e+07 5.59e+08
4  3.13e+08 -1.37e+08 5.48e+08
5  3.21e+08 -1.35e+08 5.45e+08
6  3.27e+08 -1.33e+08 5.42e+08
7  3.32e+08 -1.30e+08 5.39e+08
8  3.36e+08 -1.28e+08 5.36e+08
9  3.38e+08 -1.25e+08 5.34e+08
10 3.39e+08 -1.23e+08 5.32e+08
11 3.39e+08 -1.20e+08 5.30e+08
12 3.37e+08 -1.17e+08 5.29e+08
13 3.33e+08 -1.14e+08 5.27e+08
14 3.29e+08 -9.43e+07 5.21e+08
15 3.30e+08 -9.20e+07 5.19e+08
16 3.31e+08 -8.92e+07 5.17e+08
17 3.31e+08 -8.59e+07 5.16e+08
18 3.30e+08 -8.20e+07 5.15e+08
19 3.28e+08 -7.77e+07 5.14e+08
20 3.24e+08 -7.33e+07 5.13e+08
21 3.19e+08 -6.86e+07 5.11e+08
22 3.12e+08 -6.36e+07 5.10e+08
23 3.04e+08 -5.84e+07 5.08e+08
24 2.84e+08 -4.42e+07 5.20e+08
25 2.81e+08 -4.40e+07 5.27e+08
26 2.79e+08 -4.37e+07 5.32e+08
27 2.78e+08 -4.28e+07 5.38e+08
28 2.77e+08 -4.35e+07 5.43e+08
29 2.76e+08 -4.60e+07 5.47e+08
30 2.76e+08 -4.93e+07 5.50e+08
31 2.75e+08 -5.34e+07 5.53e+08
32 2.76e+08 -5.83e+07 5.55e+08
33 2.76e+08 -6.43e+07 5.56e+08
34 2.83e+08 -8.41e+07 5.67e+08
35 2.85e+08 -8.59e+07 5.69e+08
36 2.87e+08 -8.77e+07 5.70e+08
37 2.89e+08 -8.99e+07 5.72e+08
38 2.91e+08 -9.27e+07 5.73e+08
39 2.93e+08 -9.67e+07 5.74e+08
40 2.96e+08 -1.02e+08 5.74e+08
41 2.97e+08 -1.09e+08 5.73e+08
42 2.97e+08 -1.17e+08 5.69e+08
43 2.96e+08 -1.26e+08 5.65e+08

, , 0137

  XYZ
1  5.31e+08 5660 1.45e+08
2  5.64e+08 -330 1.47e+08
3  5.85e+08 2190 1.03e+08
4  5.35e+08 7310 9.86e+07
5  5.35e+08 7580 1.07e+08
6  5.34e+08 7780 1.14e+08
7  5.35e+08 7940 1.20e+08
8  5.34e+08 7990 1.26e+08
9  5.34e+08 7910 1.31e+08
10 5.33e+08 7750 1.35e+08
11 5.33e+08 7490 1.38e+08
12 5.31e+08 7090 1.40e+08
13 5.30e+08 6620 1.41e+08
14 5.39e+08 5470 1.50e+08
15 5.42e+08 5320 1.53e+08
16 5.44e+08 5160 1.55e+08
17 5.47e+08 4940 1.57e+08
18 5.49e+08 4610 1.59e+08
19 5.52e+08 4120 1.61e+08
20 5.54e+08 3400 1.61e+08
21 5.56e+08 2490 1.59e+08
22 5.57e+08 1450 1.57e+08
23 5.58e+08  291 1.54e+08
24 5.77e+08 -654 1.40e+08
25 5.82e+08 -335 1.34e+08
26 5.88e+08   632000 1.31e+08
27 5.92e+08  417 1.27e+08
28 5.94e+08  687 1.23e+08
29 5.95e+08  931 1.19e+08
30 5.94e+08 1150 1.16e+08
31 5.93e+08 1340 1.13e+08
32 5.92e+08 1530 1.11e+08
33 5.90e+08 1730 1.09e+08
34 5.85e+08 3280 9.65e+07
35 5.85e+08 3610 9.61e+07
36 5.84e+08 3930 9.58e+07
37 5.84e+08 

RE: [MORPHMET] Re: number of landmarks and sample size

2017-06-02 Thread Murat Maga
Just to comment.

While it is worthwhile to investigate these issues, in my experience same sizes 
are limited not because investigators are NOT willing to measure more 
specimens, but there are no additional specimens to include in the analysis, 
especially for studies based on natural populations, or historical collections.

M


From: William Gelnaw [mailto:wgel...@gmail.com]
Sent: Wednesday, May 31, 2017 3:41 PM
To: mitte...@univie.ac.at
Cc: MORPHMET 
Subject: Re: [MORPHMET] Re: number of landmarks and sample size

I'm currently working on a paper that deals with the problem of 
over-parameterizing PCA in morphometrics.  The recommendations that I'm making 
in the paper are that you should try to have at least 3 times as many samples 
as variables.  That means that if you have 10 2D landmarks, you should have at 
least 60 specimens that you measure.  Based on simulations, if you have fewer 
than 3 specimens per variable, you quickly start getting eigenvalues for a PCA 
that are very different from known true eigenvalues.  I did a literature survey 
and about a quarter of morphometrics studies in the last decade haven't met 
that standard.  A good way to test if you have enough samples is to do a 
jackknife analysis.  If you cut out about 10% of your observations and still 
get the same eigenvalues, then your results are probably stable.
  I hope this helps.
  - Will

On Wed, May 31, 2017 at 1:31 PM, 
mitte...@univie.ac.at 
> wrote:
Adding more (semi)landmarks inevitably increases the spatial resolution and 
thus allows one to capture finer anatomical details - whether relevant to the 
biological question or not. This can be advantageous for the reconstruction of 
shapes, especially when producing 3D morphs by warping dense surface 
representations. Basic developmental or evolutionary trends, group structures, 
etc., often are visible in an ordination analysis with a smaller set of 
relevant landmarks; finer anatomical resolution not necessarily affects these 
patterns. However, adding more landmarks cannot reduce or even remove any 
signals that were found with less landmarks, but it can make ordination 
analyses and the interpretation distances and angles in shape space more 
challenging.

An excess of variables (landmarks) over specimens does NOT pose problems to 
statistical methods such as the computation of mean shapes and Procrustes 
distances, PCA, PLS, and the multivariate regression of shape coordinates on 
some independent variable (shape regression). These methods are based on 
averages or regressions computed for each variable separately, or on the 
decomposition of a covariance matrix.

Other techniques, including Mahalanobis distance, DFA, CVA, CCA, and relative 
eigenanalysis require the inversions of a full-rank covariance matrix, which 
implies an access of specimens over variables. The same applies to many 
multivariate parametric test statistics, such as Hotelling's T2, Wilks' Lambda, 
etc. But shape coordinates are NEVER of full rank and thus can never be 
subjected to any of these methods without prior variable reduction. In fact, 
reliable results can only be obtained if there are manifold more specimens than 
variables, which usually requires variable reduction by PCA, PLS or other 
techniques, or the regularization of covariance matrices (which is more common 
in the bioinformatic community).

For these reasons, I do not see any disadvantage of measuring a large number of 
landmarks, except for a waste of time perhaps. If life time is an issue, one 
can optimize landmark schemes as suggested by Jim or Aki.

Best,

Philipp

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RE: [MORPHMET] number of landmarks and sample size

2017-05-31 Thread Murat Maga
I want to chime in on Mike's comment about density of landmarking changing the 
effect size. Nicolas Navarro and I did something similar in context of 
quantitative genetics of mandible shape and came to a similar conclusion using 
2D, 3D and 3D semi-landmarks sets on same dataset.

Navarro N, Maga AM. 2016. Does 3D Phenotyping Yield Substantial Insights in the 
Genetics of the Mouse Mandible Shape? G3: Genes, Genomes, Genetics 6:1153–1163.


-Original Message-
From: Mike Collyer [mailto:mlcoll...@gmail.com] 
Sent: Wednesday, May 31, 2017 7:43 AM
To: Lea Wolter 
Cc: MORPHMET 
Subject: Re: [MORPHMET] number of landmarks and sample size

Dear Lea,

I see others have responded to your inquiry, already.  I thought I would add an 
additional perspective.

Your question about statistical significance requires asking a follow-up 
question.  What statistical methods would you intend to use to evaluate 
“significance”?  If you are worried about the number of landmarks, your concern 
suggests you might be using parametric test statistics frequently associated 
with MANOVA, like Wilks lambda or Pilai trace.  Indeed, when using these 
statistics and converting them to approximate F values, one must have many more 
specimens than landmarks (more error degrees of freedom than shape variables, 
to be more precise), if “significance” is to be inferred from probabilities 
associated with F-distributions.  Therefore, limiting the number of landmarks 
might be a goal.

When using resampling procedures to conduct ANOVA, using fewer landmarks can 
paradoxically decrease effect sizes, as an overly simplified definition of 
shape becomes implied.  We demonstrated this in our paper: Collyer, M.L., D.J. 
Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for 
phenotypes described by high-dimensional data. Heredity. 115: 357-365.  This is 
consistent with Andrea’s comment about quality over quantity with the caveat 
that limited quantity precludes quality.  In other words, too few landmarks 
translates to limited ability to discern shape differences, because the shape 
compared is basic.  In the paper, we used two separate landmark configurations: 
one with few landmarks and the other with the same landmarks plus sliding 
semilandmarks between fixed points, on different populations of fish.  We found 
that adding the semilandmarks increased the effect size for population 
differences and sexual dimorphism.  But if we constrained our analyses to 
parametric MANOVA for our small samples, we would have to use the simpler 
landmark configurations and live with the results.

I do not wish to suggest that adding more landmarks is better.  Overkill is 
certainly a concern.  I would suggest though that statistical power would be 
for me less of a concern than a proper characterization of the shape I wish to 
compare among samples.  If I suspect curvature is important but am afraid to 
use (semi)landmarks that would allow me to assess the curvature differences 
among groups, opting instead to use just the endpoints of a structure because I 
am worried about statistical power, then I just allowed a statistical procedure 
to take me away from the biologically relevant question I sought to address.  
Andrea is correct that quality is better than quantity, but quantity can be a 
burden in either direction (too few or too many).  Additionally, statistical 
power will vary among statistical methods.  Reconsidering methods might be as 
important as reconsidering landmarks configurations.

Regards!
Mike



> On May 4, 2017, at 5:19 AM, Lea Wolter  wrote:
> 
> Hello everyone,
> 
> I am new in the field of geometric morphometrics and have a question for my 
> bachelor thesis.
> 
> I am not sure how many landmarks I should use at most in regard to the sample 
> size. I have a sample of about 22 individuals per population or maybe a bit 
> less (using sternum and epigyne of spiders) with 5 populations. 
> I have read a paper in which they use 18 landmarks with an even lower sample 
> size (3 populations with 20 individuals, 1 with 10). But I have also heard 
> that I should use twice as much individuals per population as land marks... 
> 
> Maybe there is some mathematical formula for it to know if it would be 
> statistically significant? Could you recommend some paper?
> 
> Because of the symmetry of the epigyne I am now thinking of using just one 
> half of it for setting landmarks (so I get 5 instead of 9 landmarks). For the 
> sternum I thought about 7 or 9 landmarks, so at most I would also get 18 
> landmarks like in the paper. 
> 
> I would also like to use two type specimens in the analysis, but I have just 
> this one individual per population... would it be totally nonesens in a 
> statistical point of view?
> 
> Thanks very much for your help!
> 
> Best regards
> Lea
> 
> -- 
> MORPHMET may be accessed via its webpage at 

[MORPHMET] RE: Survey for 3D imaging and morphometrics workshop

2017-04-12 Thread Murat Maga
Hi all,

Thanks for everyone who participated in the survey. While there is quite a bit 
of interest for using 3D volumetric data for many different biology questions, 
people seem to be frustrated with the most mundane of tasks: Getting the data 
into a format and a software that will eventually let them collect morphometric 
data seems to be a major challenge. This really surprised me. That was 
certainly an issue 15 years ago, but it shouldn’t be the case anymore.

I just started a blog (https://blogs.uw.edu/maga/) based on the SOPs of my lab 
and tutorials I used to train students. Currently it has three entries:

  1.  An introduction to the open-source 3D Slicer imaging suite, it is 
capabilities, and how to find help about it.
  2.  A long tutorial of working with data from DigiMorph (Data import, linear 
measurements, landmarking, 3d visualization, down sampling, and segmentation)
  3.  A short tutorial on getting data from MorphoSource into Slicer and how to 
fix DICOM issues.

They are not in the most appealing format, as I copied and pasted from existing 
documents, but I think they are functional enough to get an interested party 
started with his/her project. I did try to put links to the online 
documentation of every module mentioned in tutorials. If something is not clear 
from my description, you can go the source and check it out its details.

Feel free to comment and post specific questions on the blog, so that other can 
benefit from it. I would be particularly interested in knowing other imaging 
repos that cannot be imported into Slicer with the methods described in these 
tutorials. I will try to respond as soon as I can.

Hope this helps some.
M


From: Murat Maga [mailto:m...@uw.edu]
Sent: Wednesday, February 22, 2017 2:19 PM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Survey for 3D imaging and morphometrics workshop

Dear members,

If you are working (or planning to work) with 3D volumetric imaging datasets 
(such CT, or MR) and doing morphometric analyses on them, please consider 
taking this short survey  (6 brief questions) I put together. Should only take 
2 minutes. Survey will be open till March 8th 11PM, PST.

Feedback will be useful to identify the audience and sponsors for a potential a 
short course or a workshop.

https://forms.office.com/Pages/ResponsePage.aspx?id=W9229i_wGkSZoBYqxQYL0lnYz8n5LvRInWGoz5_LAC1URTZOTzdKMllOM1EyVVFZSkI2MlBRVkpKUC4u

Best,
M
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[MORPHMET] REMINDER: Survey for 3D imaging and morphometrics workshop

2017-02-28 Thread Murat Maga
Just a reminder. Survey ends March 8th.

Thanks for those who participated.


From: Murat Maga [mailto:m...@uw.edu]
Sent: Wednesday, February 22, 2017 2:19 PM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Survey for 3D imaging and morphometrics workshop

Dear members,

If you are working (or planning to work) with 3D volumetric imaging datasets 
(such CT, or MR) and doing morphometric analyses on them, please consider 
taking this short survey  (6 brief questions) I put together. Should only take 
2 minutes. Survey will be open till March 8th 11PM, PST.

Feedback will be useful to identify the audience and sponsors for a potential a 
short course or a workshop.

https://forms.office.com/Pages/ResponsePage.aspx?id=W9229i_wGkSZoBYqxQYL0lnYz8n5LvRInWGoz5_LAC1URTZOTzdKMllOM1EyVVFZSkI2MlBRVkpKUC4u

Best,
M
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[MORPHMET] Survey for 3D imaging and morphometrics workshop

2017-02-22 Thread Murat Maga
Dear members,

If you are working (or planning to work) with 3D volumetric imaging datasets 
(such CT, or MR) and doing morphometric analyses on them, please consider 
taking this short survey  (6 brief questions) I put together. Should only take 
2 minutes. Survey will be open till March 8th 11PM, PST.

Feedback will be useful to identify the audience and sponsors for a potential a 
short course or a workshop.

https://forms.office.com/Pages/ResponsePage.aspx?id=W9229i_wGkSZoBYqxQYL0lnYz8n5LvRInWGoz5_LAC1URTZOTzdKMllOM1EyVVFZSkI2MlBRVkpKUC4u

Best,
M

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[MORPHMET] MorphoJ and hidpi screen on windows 10

2017-02-07 Thread Murat Maga
Is there a way to correctly scale font size in MorphoJ on high resolution 
display?
It doesn’t seem to honor the windows’ inherent font scaling, and the default 
fonts are too small. I have to use the magnifying glass and it gets tedious 
very quickly.

M

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RE: [MORPHMET] Help with .tif files

2017-02-03 Thread Murat Maga
Alexa,
I believe Slicer reads tif files as a vector (RGB) image. You need to use 
“convert vector to scalar” module to convert it a grayscale volume. Next, you 
need to use the “editor” module to create a labelmap (binary) image that will 
be the basis for the isosurfacing operation to make a 3D model. Once you 
prepare your label map to your satisfaction, you can use the “model maker” 
module to turn it into a polygonial model, which you can save as ply, stl or 
vtk formats.

I suggest you go through their tutorials in detail on their website
https://www.slicer.org/wiki/Documentation/4.6/Training

this youtube video shows the process for an older version of slicer. Menus now 
look different, but the steps are identical
https://www.youtube.com/watch?v=og3t1i9gSG0



From: Alexa Martinez-Melo [mailto:a.mtz.m...@gmail.com]
Sent: Friday, February 03, 2017 9:22 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Help with .tif files

Hello.
I'm working with on ontogeny of irregular echinoids.
I'm able to get .tif files from CT scan, but I need 3D models in .ply format; 
when I try to get them in 3DSlicer, the software shuts down.

Could you help me with that? I need some advice, so I could start my analysis.

Have a great weekend, everyone!

--
Dra. Alejandra Martínez Melo
Departamento de Paleontología
Instituto de Geología
Universidad Nacional Autónoma de México.
(55) 5622-4283 ext. 211
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Re: [MORPHMET] Re: plotting landmarks on Morpheus?

2016-12-24 Thread Murat Maga
You can also try the markup tool in 3D Slicer (http://download.slicer.org) to 
collect landmarks. While it doesn't have the extensive mesh editing 
capabilities of MeshLab, it does have a pretty decent UI for annotation and 
measurements.


It only read stl/ply AFAIK.

M



From: Emma Sherratt 
Sent: Friday, December 23, 2016 12:15:43 PM
To: MORPHMET; dslice
Subject: Re: [MORPHMET] Re: plotting landmarks on Morpheus?

For 3D surface models, I suggest IDAV Landmark Editor 
(http://graphics.idav.ucdavis.edu/research/EvoMorph) or the commercial version 
Checkpoint that Dennis mentioned below. Meshlab's pick points function works. 
Also digit.fixed() function in geomorph R package depending on the specimens.

If you have lots of specimens, IDAV LE has an semiautomated placement system 
that is still the best IMO.

Emma
On Sat, 24 Dec 2016 at 04:37, dslice 
> wrote:
If you mean Morpheus et al., this program does not do any manual data 
collection. I have tried for years to get a scicomp student interested in 
writing such a module, but to no avail. I have written several digitizing 
programs over the decades - providing graphical feedback and interfacing to 
digitizing hardware, but cannot find the time to do this myself.

I don't need to collect data that often but for 2D data, I use tpsDig by Rohlf. 
For 3D data from meshes, I use Meshlab. That has worked sufficiently in the 
past, but not always as advertised on the Mac. Others have used Landmark 
Editor. I think the old version is free, but unsupported, while the new version 
Stratovan Checkpoint may be a commercial offering - 
https://www.stratovan.com/blog/landmark-editor

Others can chime in with their favorite data collection modality.

-ds


On Thursday, December 15, 2016 at 11:00:02 AM UTC-5, Gabriel Wrobel wrote:
I am just beginning to work with morphometrics and have a pretty simple (I 
assume) question.  I have built several 3D models of crania and mandibles using 
photogrammetry and planned to use these to plot landmark points (rather than 
using a microscribe) suing Morpheus.  But, I can't figure out how to place the 
landmark points on the model.  I was unable to find (recognize) this 
information in the user's guide.

What I would love, in fact, is a very general explanation of how to get started 
building a database.  The user's guide seems to start with the analyses, and 
assumes a basic level of familiarity that I sadly don't have.

Any and all suggestions are appreciated!

Gabe








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Re: [MORPHMET] RE: micro-CT suggestions

2016-12-06 Thread 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 <tomomaho...@gmail.com>
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 
<angela.rogg...@unito.it<mailto:angela.rogg...@unito.it>> 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 <morphmet@morphometrics.org><mailto:morphmet@morphometrics.org>
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<tel:(618)%20650-2394>
Fax:  (618) 650-3174<tel:(618)%20650-3174>
e-mail:  lk...@siue.edu<mailto:lk...@siue.edu>





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&qu

[MORPHMET] RE: micro-CT suggestions

2016-12-05 Thread Murat Maga
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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RE: [MORPHMET] Re: Problem with missing data using MorphoJ

2016-11-13 Thread Murat Maga
MorphoJ handles missing landmarks, but I don't think it has a function to 
estimate them. SO without an estimation of your landmark position, your options 
are either to drop the sample from the analysis (if you want to retain full set 
of landmarks) or to remove the landmark from your analysis (to keep full set of 
individuals). 

You can also experiment with trying to estimate them based on reflection (if it 
is a symmetrical structure) or based on bunch of reference samples. Both Morpho 
and gemorph in R have functions for estimating missing landmarks. See if they 
give you reliable estimates, and then you can proceed with your analysis. 

Otherwise your options are limited to those two.
M


-Original Message-
From: Rosa Perez [mailto:rmper...@ncsu.edu] 
Sent: Saturday, November 12, 2016 9:53 PM
To: MORPHMET 
Subject: [MORPHMET] Re: Problem with missing data using MorphoJ

On Thursday, August 11, 2016 at 4:06:01 PM UTC-4, Jade Racine wrote:
> Dear all,
> 
> 
>  
> I digitized 108 craniofacial landmarks on human skulls from an 
> archaeological context using a MicroScribe G2X. I have a lot of random 
> missing values due to postmortem damage. I am currently trying to 
> analyze my data using MorphoJ. I followed the instructions from the 
> user’s guide, entering "-" in the data files for missing values. I 
> then combined the dorsal and ventral views using FileConverter. The files I 
> get can be read in MorphoJ.
> However, nothing else works. I can’t visualize the landmarks or 
> perform any kind of analysis. If I try to find outliers, I get the 
> message "Finding outliers is not possible because only a single 
> observation or none at all is available". I get this message 
> regardless of whether I upload one file with all individuals in it or 
> multiple files with one individual each. The problem seems to be with 
> the "-" code because if I remove the missing landmarks from my 
> data files, MorphoJ runs correctly. I tried to substitute "-" for 
> "" or "-999". MorphoJ runs fine with those but generates odd 
> results that do not look like the shape of a skull. I really want to 
> be able to analyze my dataset with missing values, otherwise I lose 
> too much landmarks and I can’t afford to remove individuals since my 
> sample is already small. Does anyone know what I am doing wrong or how I can 
> fix the problem? I attached an example of my data files.
> 
> 
>  
> 
> 
> Any help would be greatly appreciated.
> 
> 
> Thank you,
> 
> 
>  
> 
> 
> Jade Racine
> 
> 
> Master’s student
> 
> 
> Department of Anthropology
> 
> 
> University of Montreal, Canada

Hi Jade,

I am also a masters student attempting to use MorphoJ and am having a difficult 
time with the missing data. I collected 3D landmarks for a cranial asymmetry 
project and cannot get MorphoJ to run. It keeps giving me an error message. Did 
you happen to figure out what the issue was? I would truly appreciate any 
advice you might be able to share.

Thank you,

Rosa Perez
Masters Student
NCSU
Dept of Anthropology

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RE: [MORPHMET] problems opening ply files

2016-11-01 Thread Murat Maga
I am not sure what you mean Meshlab opens, but not displays it. Do you actually 
see information about your model in meshlab? If you see information about your 
model, it opened it. Perhaps faces are inverted. I have seen proprietary 
software (such as 3DMD) not exporting ply/stl properly from their own format.

If you can’t open it with Meshlab, chances are good that your model is 
misconstructed. I don’t think it is anything to do laser vs photogrammetry.

M




From: Gabriel Wrobel [mailto:gwrobe...@gmail.com]
Sent: Tuesday, November 01, 2016 12:48 PM
To: MORPHMET 
Subject: Re: [MORPHMET] problems opening ply files

I am running Morpheus with .bat, and tried the Meshlab workaround, and still no 
luck opening my cranial model.  I tried saving it both with and without texture 
-- neither worked. I also tried saving it as an obj file, and it also doesn't 
open. Meshlap seems to read the files, but just never opens them. I was 
wondering if anyone else using Morpheus has tried working with ply files made 
with photogrammetry (rather than laser scanning). Many thanks!

gabe

On Friday, October 28, 2016 at 1:47:30 PM UTC-4, dslice wrote:
Two possibilities...

1) Make sure you are using the latest version and running the program
via a .bat, .sh, or .app. There could be memory problems if you try to
run the .java file directly. The scripts provide for more memory.

but more likely...

2) Some programs create .ply files that are somehow indigestible by
Morpheus. Open the file in Meshlab and (re)save it (binary or ascii
doesn't matter). That might clear up any problems.

-ds

On 10/28/16 1:37 PM, Gabriel Wrobel wrote:
> Hi all.  I am new to this sort of analysis, so apologize in advance for
> the rudimentary nature of my question. I am attempting to open ply files
> of 3D cranial models built with Agisoft Photoscan on Morpheus and am not
> having any luck at all. Morpheus reads the file, but does not open it.
>  It seems to be fine with ply files created from laser scans.  Is this
> an issue anyone is familiar with? Thanks!
>
> gabe wrobel
>
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RE: [MORPHMET] placePatch in Morpho (R)

2016-03-10 Thread Murat Maga
Yes, copy all your meshes to a folder, and pass the path to it to placePatch. I 
thought I used binary stls as well, but I might be mistaken.
Make sure the Z dimname (or sample name) in the p.k.n array matches the 
filenames (minus .ply) since I think I that’s what it uses to match the LM 
array to the mesh.

M



From: morphmet@morphometrics.org [mailto:morphmet@morphometrics.org] On Behalf 
Of Pere Ibáñez
Sent: Thursday, March 10, 2016 7:38 AM
To: MORPHMET 
Subject: [MORPHMET] placePatch in Morpho (R)

I am using the function placePatch in Morpho: placePatch(atlas, dat.array, 
path, prefix = NULL, fileext = ".ply", ray = TRUE, inflate = NULL, tol = 
inflate, relax.patch = TRUE, keep.fix = NULL, rhotol = NULL, silent = FALSE, 
mc.cores = 1). I already created the atlas using createAtlas, and I checked 
using plotAtlas and it looks fine.

In placePatch, in path, I am supposed to specify the directory where the 
surface meshes of the sample are stored. Does this mean that I have to specify 
the folder where all the 3D images are? In that case, must they be in a 
specific format? Ascii PLY maybe?

I tried specifying the folder where my images are, but it didn't work (I 
obtained a pxkxn array with only missing values -NAs-). May this occur because 
my images are Binary PLY?

Thanks in advance!

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RE: [MORPHMET] Multivariate Analysis of Genotype-Phenotype Association

2016-02-26 Thread Murat Maga
Actually, on the same topic I would also like to announce our new paper in G3.

Navarro N and Maga AM. 2016. Does 3D Phenotyping Yield Substantial Insights in 
the Genetics of the Mouse Mandible Shape?
Available early online at
http://www.g3journal.org/content/early/2016/02/22/g3.115.024372.abstract

We revisit the early investigations of mandible genetics through geometric 
morphometrics and demonstrate the gain-of-information when 3D morphometrics is 
used along with dense landmarking. We also favor a true multivariate analyses 
that uses all phenotypic traits, as oppose to mapping them individually.

The R package for the shape mapping (R/shapeQTL) is available through Dr. 
Nicolas Navarro’s website (http://nnavarro.free.fr/) and also on github. 
(https://github.com/nnavarro/shapeQTL)

Best,
Murat




From: mitte...@univie.ac.at [mailto:mitte...@univie.ac.at]
Sent: Thursday, February 25, 2016 7:40 AM
To: MORPHMET 
Subject: [MORPHMET] Multivariate Analysis of Genotype-Phenotype Association

I would like to announce a new paper, of which the early view pdf is already 
online.

Mitteroecker P, Cheverud JM, Pavlicev M (2016) Multivariate Analysis of 
Genotype-Phenotype Association. Genetics

http://www.genetics.org/content/early/2016/02/18/genetics.115.181339

It offers an exploratory strategy for mapping multivariate data and is 
particularly suited for geometric morphometrics. The new method identifies 
patterns of allelic variation (genetic latent variables) that are maximally 
associated - in terms of effect size - with patterns of phenotypic variation 
(phenotypic latent variables). It thereby separates phenotypic features under 
strong genetic control from less genetically determined features and thus 
permits an analysis of the multivariate structure of genotype-phenotype 
association, including its "dimensionality" and the clustering of genetic and 
phenotypic variables within this association.

Best,

Philipp Mitteroecker
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[MORPHMET] template based automated landmarking

2015-12-08 Thread Murat Maga
Hi all,

 

Apologies if you received this e-mail twice. Last time it bounced back to me
saying I am not subscribed to the list. Weird.

 

I want to bring our recent contribution on template based landmarking to
your attention. It is an open article available at
http://www.frontiersinzoology.com/content/12/1/33

We are looking for published microCT datasets to evaluate it further. Please
contact me if you are interested in collaborating.

 

Young R, Maga AM. 2015. Performance of single and multi-atlas based
automated landmarking methods compared to expert annotations in volumetric
microCT datasets of mouse mandibles. Frontiers in Zoology 12:33. 

 

M

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