We will be photographing subjects (barn owls) with a DSLR. The white balance will be calibrated using a white balance card at each nest box instead of batch post-processing. Each photo will capture an individual’s ventral surface then cropped to a 60x40mm rectangle at the same spot on the breast (sample below) for measuring average plumage color (RGB values), number of spots per cropped breast image, and the average vertical diameter of the breast spots in the cropped image.
Here is what we would like to do through Fiji:
Is it possible to automate the cropping process by creating a macro that will crop all the images to a 60x40mm rectangle? → Will need to include some sort of scale bar (e.g. 40mm) in a different color that won’t be in the photo (e.g. blue)?
Is it better to:
2a) write a macro that generates the RGB values for 5-10 random areas, excluding the black spots, and average those values to obtain one RGB value per individual or at the very least provide some output with the 5-10 RGB values per photograph that we can then average in another program; or
2b) develop a macros that will output an RGB value for the entire non-spotted area of the cropped breast image?
*If we go route #1^^, do we manually move our random ROIs if they contain a spot simply by dragging the ROI?
Would a macro be able to identify all the black spots in the cropped image, measure their vertical diameter, and average all the spot measurements to get an average spot diameter measurement for each individual?
3a) With this process, is it better to first create a binary image (spots & no spots) and then measure the vertical diameter of every spot?
3b) Will we have to manually remove spots that fall on the edge of the 60X40mm cropped photo? If so, how do we do that?
With spot quantity:
4a) Should we create a binary image (spots & no spots) or just leave as is and count the number of spots?
4b) Will we have to manually remove spots that fall on the edge of the cropped image so they are not counted or is there a way to automate that in the code? If we do have to do that manually, how would we do that?
We are just starting out with Fiji and would really appreciate any help. Thank you so much in advance!