Thanks. I am definitely considering whether it is worth the work to rectify the values. Most of the time I see CS it is simply a proxy for size, and I have skull and other lengths in hand.
On Friday, October 18, 2024 at 9:48:41 PM UTC-7 Murat Maga wrote: > Before you do anything first decide whether the orders of magnitude > difference in CS is going to be relevant. Procrustes analysis will > uniformly scale the coordinates using the centroid size from each specimen, > so they all will have unit size. So, from analytical point of view there is > no harm if you are only going to use the procrustes aligned coordinates or > PC derived from them in your analysis. The moment you will run into issues > is when you include the actual centroid size as a variable in your > analysis, whether for allometric regression or for simply using it species > comparison. Imagine a case where you have two specimen of the same species, > one with centroid size in thousand (because probably the coordinates are in > raw pixel distances) versus one it is in tens (because probably same > scaling has been already applied to the image either directly or > indirectly). That obviously wouldn't make much biological sense. > > If you had ruler visible in all your images, proper way to correctly scale > the data is to measure a known distance (e.g., 50mm) in ImageJ and look at > the length reported in pixels (e.g., 500 pix). Then the correct scale of > data is 10pixels/mm (or in other words 100 micron resolution), which you > can apply using the menu you have shown in your screenshot. This of course > assumes the measured distance is more or less parallel to one of the image > axes. The more off-axis it is, the more error you will make. If the field > of view and the image resolution didn't change between acquisition, then > you probably only have to do this on a few samples, and if they are all > coming out around the same value, you can use that as your the scaling > coefficient for the remaining samples without having to measure them. > However, if the field of view has changed (zoom in/out), or you changed the > resolution of the images after the acquisition you can't rely on your one > size fits all type of scaling, and have to go one by one. There are three > orders of magnitude difference in your centroid size plot, so it is hard to > tell whether the clusters around thousands range are due to different image > acquisition parameters, or natural size variation (which might be the case > if you kept all the imaging parameters the same and your specimens vary > quite a bit in size). All I can say, you definitely have minimum of two > groups for sure (thousands range, and the ones close to zero). The rest you > have to decide by trial and error. > > Again, if you are not planning to use centroid size anywhere in your > analysis, then all this is moot. You can stick to procrustes coordinates > based shape analysis, and all will be good. > > > > On Friday, October 18, 2024 at 3:40:27 PM UTC-7 Chris J Conroy wrote: > >> Hello morphologists, >> >> I’ve created a landmark dataset for ~250 mammal skulls. My process >> was to take images in the same view, with a ruler in the image. I opened >> the files in ImageJ and plotted the points. I’ve made an input file in >> MorphoJ and done the usual analyses, which largely make phylogeographic >> sense. However, centroid size appears to be in semi-discreet bands of >> values ranging from near 0 to near 4000. I’m sure the variation comes from >> at least two sources. One is that I used two cameras, one at 72 DPI and the >> other at 96 DPI. Opening the images in Mac Preview allows me to check this. >> Next, in ImageJ, it looks like for some of them I set a scale based on the >> image density and others I did not. The landmark XY values themselves >> differ by orders of magnitude. >> >> I took a sample of specimens from top to bottom of the centroid size >> variation and fixed the scale in ImageJ and recreated the landmarks. The XY >> values are now in the same range. >> >> Before I sit down and do this for all 250 images, I wanted to see if this >> is going to be a waste of time, or will images from different digital >> cameras going to be fundamentally different in centroid size and not worth >> the work. I suppose I could do the work and then code all the images by >> camera and see if there is an obvious effect. Surely I’m not the first >> person to go through this. >> >> If it comes to it, I can re-take the lower res images on the higher >> resolution camera. >> >> Lastly, on the higher resolution camera, some images are slightly zoomed >> to fill the image with the object. Will this also mess up centroid size? >> >> Thanks, >> >> Chris >> >> >> >> -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/a0e37ac2-ec6b-4495-9ce3-5bcc28657e63n%40googlegroups.com.
