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
samples

(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 

[MORPHMET] Re: Digital morphology data survey results - desire for centralized digital repository

2017-08-15 Thread Douglas Boyer
Dear Christy and Emma:

Thanks for conducting this survey!  Its great to see the enthusiasm for and use 
of digital data!  I was surprised by the strong interest in centralized digital 
repositories.  

I am the founder and director of MorphoSource (www.morphosource.org) and we are 
planning to begin a massive scaling of our infrastructure thanks in part to 
major NSF funding 
(https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661386=false)
 and matching commitments from other sources.  Part of our long term plan for 
sustaining growth of the archive involves recruiting help from other 
institutions for distributing storage needs in a cloud-like fashion.  Some of 
the details of this plan (explaining the mutual benefits of such an 
arrangement) as well as a description of many of the basic features of 
MorphoSource are available here 
(https://www.researchgate.net/publication/316669746_MORPHOSOURCE_ARCHIVING_AND_SHARING_3-D_DIGITAL_SPECIMEN_DATA).
  

Many of the features that people were hoping for in a digital archive according 
to survey responses (DOIs, metadata describing ownership, better searching and 
downloading, restricting use during embargo periods, tracking use after) are 
already implemented on MorphoSource and being used.  It is designed not only to 
serve the interests of users in getting data, but also the interests of 
contributors and curators in regulating and tracking data use. 

A critical component of any architecture for an open use 3D database is 
maintaining relationships between raw and successive derivative versions of 
datasets. All such relationships can be maintained in a straightforward way in 
our infrastructure when uploading either new data or data derived from existing 
datasets on the archive.

Furthermore, our team is coordinating with a number of other groups in 
developing a standard data vocabulary (probably as an extension of Audubon 
Core) for describing and sharing such data. 

MorphoSource currently hosts almost 30,000 datasets representing 3D scans of 
~7000 specimens from 150 different museums.  We are also beginning a 
collaboration with 15 museums across the US to add another 20,000-30,000 
specimens ('oVert' an NSF TCN led by David Blackburn at UF, Gainesville).

Best,

Doug :)


On Friday, August 11, 2017 at 2:06:11 AM UTC-4, Christy Anna Hipsley wrote:
> Dear Morphmeters,
> 
> 
> The digital morphology data survey posted here 2 weeks ago is now closed, and 
> we thank you immensely for your overwhelming (117!) responses. 
> 
> 
> For a graphical summary of those answers, please click here. 
> 
> 
> Next week I will present these results together with a literature survey on 
> the impacts of digital morphology in systematic research at the BioSyst.EU 
> meeting in Gothenburg, Sweden. After that we will be working to put this 
> information into a broader context with recommendations on how we can 
> practically move forward as a community to ethically source and disseminate 
> our data, based largely on your feedback. At first glance it's clear that 
> issues like author acknowledgement, access, resources, and institutional 
> policies will play major roles in this endeavour.  
> 
> 
> 
> 
> As a simple illustration, below is a word cloud based on your responses to 
> the question "What do you see as the biggest obstacles to obtaining digital 
> morphology data?".
> 
> 
> 
> 
> We will continue to post our findings here and again we thank everyone for 
> their time and feedback.
> 
> 
> Best wishes,
> Christy & Emma
> 
> 
> 
> 
> 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 

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