Hi Zack, In addition to Carmelo's points I'll add that I've just posted a tutorial showing how to use my R package StereoMorph to collect 2D landmark and curve data (http://home.uchicago.edu/~aolsen/software/digitizing.shtml). The digitizing application allows you to scale your shape data using either a checkerboard pattern (including via automated detection) or points on a ruler. The tutorial also shows how to read the landmark data into R for morphometric analyses.
As far as cameras/lenses, I use a Nikon D5000 with an 18-55 mm lens. I always zoom in the lens to 55 mm and then move the camera to change the frame size. I tested for distortion with a checkerboard pattern and when zoomed to 55 mm it is on the order of microns (negligible for my purposes). It's good to make sure at the outset that your lens isn't introducing distortion. Also, another advantage for using a solid background (especially black velvet) is that it reduces the file size (because noise increases file size) while allowing you to keep a high-res image. That can make a big difference when you're taking hundreds of images - it's nice when you can fit everything on a single external hard-drive (plus back-up!). You can get cheap black velvet at a fabric store for about $10/yard. Hope that helps, reply if you have any questions, Aaron Aaron M. Olsen PhD Student Organismal Biology & Anatomy, University of Chicago Bird Division, Field Museum of Natural History home.uchicago.edu/~aolsen/ On Friday, June 5, 2015 at 2:11:18 PM UTC-5, Zack Daugherty wrote: > > > Hello all, > > This is my first time wading into geometric mophometry as a PhD candidate. > > First off the project: > I plan to track geometric morphometry data of Nassau grouper we have > raised in the lab. There are some 130 juveniles that are now capable of > being anesthetized and handled. I plan to gather data down to the > individual level for this cohort monthly to establish data on individual > ontogenetic trajectories. But I have some questions regarding 2D capture, > because *once I start this there is no going back*. The welfare of these > animals supercedes the morphometry work I have planned (these fish will be > used for future broodstock at our aquaculture facility). > > Resources I have read on 2D capture setup are: > - Geometric Morphometrics for Biologists: A Primer 2nd Ed. (Text and Supp. > Workbook) > - RHOI Photography Protocol > - Scoured archives of this listserv using tags "capture", "image", "2D" > > In preparation I've purchased (keep in mind extreme budget restrictions): > - Olympus Tough TG-4 <http://www.getolympus.com/us/en/tg-4.html> > (Personal Camera, External Viewfinder capabilities to smartphone/tablet, > RAW mode) *unable to obtain a nice DLSR at this time* > - RPS Lighting RS-C150 Copy Light Set (110V) > <http://www.bhphotovideo.com/c/product/438355-REG/Dot_Line_RS_C150_RS_C150_Copy_Light_Set.html> > - RPS Lighting 12 x 18" Desktop Copy Stand > <http://www.bhphotovideo.com/c/product/686878-REG/Dot_Line_RS_CS380_12_x_18_Desktop.html> > - 2 Sylvania / Osram 211 (75W/120V) Lamp > <http://www.bhphotovideo.com/c/product/815036-REG/Sylvania_11657_PH211_Lamp_75W_120V.html> > - Rite in the Rain 1140 All-Weather Metric Cross Section 2mm Grid Pad, > 8.5" x 11" > <http://www.rainwriter.com/RiteintheRain-1140-Metric-Cross-Section-2mm-Grid-p/ritr-1140.htm> > - Dissecting Pad, Vinyl, Deluxe, 11 3/4 x 8 in > <http://www.carolina.com/dissecting-pans-pads/dissecting-pad-vinyl-deluxe-11-34-x-8-in/629006.pr?catId=&mCat=&sCat=&ssCat=&question=dissecting+pad%2C+vinyl%2C+deluxe%2C+11+3/4+x+8+in> > - Living Systems Instrumentation PIN-#3 Stainless Steel Insect Minuten > Dissection Pins, Size #3 > <http://www.amazon.com/gp/product/B00J5Q7YCC?psc=1&redirect=true&ref_=oh_aui_detailpage_o02_s00> > - Incra Rules 150 mm Precision Metric Marking Rule (Stainless Steel) > <http://incra.com/product_markingrules.htm> > > I'm attaching a couple photos of the copystand setup and a tagged, > anesthetized grouper (not under ideal camera setup for morphometry work, > just a quick snap with iphone after tagging). > > Testing a few juveniles I am able to anesthetize them heavily where they > are completely immobolized; however, I plan to place pins posterier of the > anterior-most spine tips of the dorsal and anal fins, and behind the pelvic > (not through the tissue), into the grid paper that is on top of the vinyl > dissecting pad all mounted on the copystand. I also plan to capture both > right and lefthand sides of the animals because several have opercular > deformities on one or both sides. I have not yet tested this with the > anesthitized fish, I have only anesthitized them to test an elastomer > tagging method (which works quite well using only 29g insulin needle). > > There is a multitude of information of what to do with landmark data, but > not much with respects to the actual photography itself. I just want to > make sure I go into this with the most information possible. > > The primary question I'm wanting to ask here is whether there are any good > protocols I've missed or recommendations from people experienced with 2d > capture of largely 2d fish or very low profile specimens. I've seen some > people surround their specimen with black material to, what I guess, is a > method to reduce diffuse light through the aperature. > > I have planned to practice with a aperature of ~f4.0. I noticed that RHOI > recommends >f8.0 with f32.0 prefferable which is far beyond the scope of > this camera. Default, no zoom wide is f2.0, f2.8, f8.0 and under optical > zoom f4.9, f6.3, and f18.0. As soon as the metric grid paper comes in I > plan to following the *Checking your system* section of the Geometric > Morphometrics for Biologists, pg. 12-13 to determine where the distortions > in the camera setup lie under different zoom/aperature settings. > > Questions: > Any other protocols that people are aware of I should look at for digital > capture? > Should I surround my specimens in black material? > Should I purchase any white balance card sets? > Would a grid backdrop be neccessary for every photo behind the specimen or > just to initially calibrate a field a view before photographing specimens? > > Thanks for the great opportunity to become a part of this forum. > > - Zack > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
