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Hello there!  I've been working with a very small mammal skull (a tenrec) and can't seem to get it right in that the top and bottom are not recognized in one single chunk in Agisoft.  I can only get the photos to align in separate chunks, which is a huge headache.  I've been using a turntable, diffuse lighting, tripod, remote shutter, changed the background after flipping the skull over and masked everything.  I suspect it's my photos that are causing the problem...and I might need a bit more light, (the lab I was in was a bit dark).  The size of the skull is about 1.25 inches in length, 1/2 inches in height, and 1/4 - 3/8 inches in width.   Should I shoot one circuit at 50mm and another at 24mm?  This first attempt was with a Canon T3i with a standard lens set at 24mm.  Camera settings were ISO at 200, F7.1, shutter speed 1/80.   Does anyone have any advice on shooting something this small?  Thank you in advance for your help!

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Failure to align 2 sections together if you have masked the images is usually due to a lack of overlapping detail between the two sets of images.  For very small objects, differences in focus can also be problematic, especially on turntables and an object with a high length:width ratio.  When planning a shoot I pick where the join between the 2 sections will be on the object and then position it so that I can ensure that images in both sets provide adequate coverage across this area.  In the case of complex objects you may find that 2 orientations is not enough and you may need to shoot 3 or 4.  To ensure focus overlap as well I either shoot focus stacking (rarely) or shoot handheld and move around the object so that I can carefully position the plane of focus.

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You might also try stopping down even further to F11, to get a better depth of field. The other issue is whether the skull has enough details on it for Photoscan to be able to match points between different photos. If not, you might try shooting RAW, then increasing contrast/clarity in the photos to accentuate whatever details are present.

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