Dear Murat, Thank you very much for your email and time for explore my dataset. To perform this simple experiment, given the aim was to explore the magnification issue, I chose only three landmarks (as you could see in the tps file) easily to replicate. The reason I am trying to combine two magnification is that I will work with groups with different sizes; for example, species with 10 cm and others with 3 cm of total length of skull. Place the camera at a good distance to avoid parallax for the large group will lead a low resolution images of the small groups. Thus, my initial idea was to have two standardized distances and combine later after accounting the scale effects.
In my short experiment, what intrigues me is the clear groups in PCA (and other exploratory analyses) based on the two magnifications (see below). At the beginning, I was expecting a great overlap between the two distances and minimum differences due to landmarks-placement error as seen within each of the group. Best, Anderson [image: Inline image 1] On Sat, Dec 30, 2017 at 3:57 PM, Murat Maga <m...@uw.edu> wrote: > 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 > > > > > > *From:* Anderson Feijo [mailto:andefe...@gmail.com] > *Sent:* Friday, December 29, 2017 1:35 AM > *To:* MORPHMET <morphmet@morphometrics.org> > *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 > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- _____________________________________________ Dr. Anderson Feijó Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Science Beichen West Road, Chaoyang District, 100101 Beijing, China Curriculum: *Lattes <http://lattes.cnpq.br/9406413385468571>; ResearchGate <https://www.researchgate.net/profile/Anderson_Feijo>* -- 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.
