[MORPHMET] Job opening in vertebrate anatomy

2018-11-12 Thread Novack-Gottshall, Philip M.
Hi all,

See below for a possibly paleo-relevant job opening. Feel free to
contact me with general questions, but for search-related questions,
please contact our assistant Krista Frickelton (e-mail below), who will
forward to the search chair.


Open Tenure Track Position, Biological Sciences
Appointment to begin Fall 2019

The College of Science at Benedictine University invites applications
for a full time, tenure track assistant professor position in the
Department of Biological Science beginning fall 2019. The department is
seeking a candidate who has research interests and teaching expertise in
at least one of the following areas: biomechanics, vertebrate biology,
evolutionary or developmental biology. The position requires teaching a
cadaver-based anatomy course and other courses within our core
curriculum. The successful candidate will establish and participate in
faculty/student research at the undergraduate level. Candidates are
expected to maintain an active research program.

The Department of Biological Sciences consists of 15 full time faculty
members and houses three undergraduate biology programs: BS in Biology,
BS in Health Science, and BA in Biology. There are over 600
undergraduate majors in the department with the majority of students
seeking to pursue professional health degrees. We also have two Master’s
programs in Clinical Exercise Physiology and Integrative Physiology. Our
current faculty have expertise in physiology, ecology, microbiology,
neurobiology, molecular biology, genetics, biological anthropology, and

Founded as a Catholic university in 1887, Benedictine University is
located in Lisle, Illinois 25 miles west of Chicago with additional
campuses in Mesa, Arizona and Springfield, Illinois. Benedictine
University seeks employees who, regardless of their religious
affiliation, understand and contribute to the University’s mission and
goals. As an institution, we are committed to our identity as Catholic
and Benedictine in our values, our operations, and our curriculum in an
effort to help each student, each employee, the local community, and
each other thrive academically, professionally, and personally in our
religiously and culturally diverse academic environment. The College of
Science enjoys a location in the research corridor of metropolitan
Chicago, and delivers nationally recognized undergraduate programs in
the sciences.

Required Qualifications: Earned Ph.D.; a minimum of one year
postdoctoral experience is preferred. Successful prior experience
teaching undergraduates and a strong commitment to involving
undergraduates in research are required.

Application Deadline: Applications will be accepted until the position
is filled, but priority will be given to those applications received by
December 17, 2018.

Application Process: Interested applicants should submit a cover letter,
curriculum vitae, names of five people who can be contacted
confidentially as references, unofficial graduate transcripts, statement
of teaching philosophy, and statement of research interest through
Academic Jobs Online at http://academicjobsonline.org/ajo. Any questions
regarding the application process should be directed to: Krista
Frickelton, College of Science, Benedictine University, 5700 College
Road, Lisle, IL 60532. Email: kfrickel...@ben.edu Fax: (630) 829–6547.

Benedictine University does not discriminate in its admissions or
educational policies, programs or activities; scholarship and loan
programs; athletic and other University administered programs or
employment practices on the basis of race, creed, color, national
origin, sex, sexual orientation, age, disability, military or veteran
status, marital status, citizenship, or any other characteristic
protected by applicable law. The laws applicable to Benedictine
University include constitutional and statutory protections of the
University's rights as a religiously sponsored institution. This policy
of equal employment opportunity applies to all employment and personnel
practices including, but not limited to, recruiting, hiring, promotion,
training and compensation.

In compliance with federal law, all persons hired will be required to
verify identity and eligibility to work in the United States and to
complete the required employment eligibility verification document form
upon hire.
Benedictine University is an Equal Opportunity Employer

   Phil Novack-Gottshall, PhD
   Department of Biological Sciences
   Benedictine University
   5700 College Road   Lisle, IL 60532

   Office: 332 Birck Hall
   Lab: 316 Birck Hall
   Phone: 630-829-6514
   Fax: 630-829-6547

   Fall 2018 office hours:  Tues/Thurs 9-9:30, 1:30-2:30
   Wed 10-10:30, 11:30-12:15 & 

[MORPHMET] Computing a species average from a set of landmarks

2018-11-12 Thread Grace Capshaw

Hi all,

I am currently using Landmark IDAV to place landmarks onto .ply mesh files, 
but when I try to compute a species average from several meshes the 
software crashes. This happens even when I reduce the number of mesh files 
to be averaged, and when I use the "Low Resolution" output option. Has 
anyone run into this issue (and ideally, figured out how to fix it)? If 
not, can anyone recommend a (free) software or R package that can compute a 
species average from a set of landmarks?

Thanks very much for your help!


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Re: [MORPHMET] Re: semilandmarks in biology

2018-11-12 Thread Douglas Boyer
And not to deflect it further, but as long as we are now speaking of
automation of landmarking and its implications for transformational
homology hypotheses, people may be interested in some of the perspectives
and results of this paper on "fully automated" landmarks for diverse shape

(e.g., claw to nail or gorilla to mouse lemur).

... here is a recent update using a gaussian process for spreading landmarks
 that emulates human landmarkers in
many cases (see Fig. 1).

...an example of using geometric similarity
 to test homology hypotheses (see
Fig. 3)

On Mon, Nov 12, 2018 at 2:00 AM Murat Maga  wrote:

> This has been an interesting discussion. Hopefully it has been useful to
> the newcomers to the GMM and shape analyses to better understand some of
> the challenges they are likely to face. I think the issues of homology,
> semi-landmarks, number of variables vs number of samples routinely
> discussed here because ultimately there is no hard rule to abide by, but
> realities to live with (sample sizes may not be increased) and trade-offs
> to be made. I like Benedikt's argument about biological pragmatism.
> I do not want to hijack the thread and the topic, but wanted to briefly
> reflect on Benedikt's comments atlas based methods. Image based analyses,
> when coupled with a computationally derived anatomical atlas, do offer a
> promise of automating some aspects of the acquiring information on
> morphology from volumetric scans. This approach can be particularly
> powerful, and appealing if one is working with a very large number of
> individuals (>>100) of the same species and of similar developmental stage.
> I find this approach very useful in tedious preprocessing steps
> (segmentation, rigidly aligning samples to a fixed anatomical orientation
> say to make standardized 3D renderings of all samples to visually assess
> phenotypic variability, etc), basically in processes that can tolerate
> large margin of error. Whether they can fully replace landmark based
> analyses (or result in fully automated landmarking procedures), I am not
> entirely sure. Basically, it boils down to the fact that there is no
> independent assessment of how well the registration performed, apart from
> the visual inspection of how well the template deformed into the sample (or
> the other way around depending on the task). The choice of image similarity
> metrics (along with many other parameters than can be tuned) can result in
> different outcomes. Even in the well-chewed domain of human neuroimaging
> validation of non-linear image registration remains a big issue. They
> typically resort to ranking algorithms on how well they approach to the
> manually segmented reference datasets. Since atlas-based landmarking is
> essentially an image segmentation process, we do need to assess how well
> registration simulated the human observer's landmark placement if we are to
> justify using one method over another.
> While, I agree with Benedikt's comment "measure the biological effects of
> interest rather than how well they simulate the behavior of manually placed
> landmarks" in principal, I am not entirely sure how one can go about this
> without knowing what the biological effects of interests are beforehand,
> because we wouldn't know what we measured.
> M
> -Original Message-
> From: Benedikt Hallgrimsson 
> Sent: Thursday, November 8, 2018 11:32 AM
> To: Adams, Dean [EEOBS] ; andrea cardini <
> alcard...@gmail.com>; morphmet@morphometrics.org
> Subject: RE: [MORPHMET] Re: semilandmarks in biology
> Dear Colleagues,
> So I’ve been wondering whether to wade into this issue..
> There seems to be an undercurrent here of mathematics vs biology, but I
> suspect that the real issue here is probably morphometric theory versus the
> pragmatic compromises necessary when using morphometric tools to answer
> biological questions.  Others on this thread have thought (and written)
> much more deeply about the interface of morphometric theory and biology
> than I have, but for what it’s worth, here are my two cents on this issue.
> Fundamentally, what is most important is that quantifications of morphology
> capture relevant biological variation while avoiding artifacts that can
> skew or mislead interpretation. That matters much more to than whether
> there is real homology or not. I'm not even sure what "real homology" for
> landmark coordinate data means in a biological sense, even for Type 1
> landmarks.  The "identity" or homology of landmarks tends to become messy
> pretty quickly when the underlying developmental biology is examined
> closely. I think Paul O'Higgins gave a great talk once on that basic theme
> if I remember correctly. Chris Percival also did a nice analysis showing
> how apparently