- Why does the
Patch Shapeneed to be a multiple of 16 instead of 8 for the Fiji implementation?
In ZeroCostDL4Mic, they allow the
patch_heightto be factors of 4 which lets me do 3D N2V on my z-stacks with less than 16 planes.
# Here we check that patch_size is divisible by 8 if not patch_size % 8 == 0: patch_size = ((int(patch_size / 8)-1) * 8) print (bcolors.WARNING + " Your chosen patch_size is not divisible by 8; therefore the patch_size chosen is now:",patch_size) # Here we check that patch_height is smaller than the z dimension of the image if patch_height > Image_Z : patch_height = Image_Z print (bcolors.WARNING + " Your chosen patch_height is bigger than the z dimension of your image; therefore the patch_size chosen is now:",patch_height) # Here we check that patch_height is divisible by 4 if not patch_height % 4 == 0: patch_height = ((int(patch_height / 4)-1) * 4) if patch_height == 0: patch_height = 4 print (bcolors.WARNING + " Your chosen patch_height is not divisible by 4; therefore the patch_size chosen is now:",patch_height)
- If my 4D datasets feature photobleaching, what’s the best course of action?
My gut instinct is to compensate for this by having my training set includes z-stacks from many different time points. I would not think that doing a bleach correction and then N2V would lead to good results.