How to approach excluding holes above a set threshold
I am trying to get the size/area of sections of lung tissue. As this tissue essentially looks like a sponge, there are numerous holes (the part of the lung containing air). Many tissue sections also contain large blood vessels that also appear as empty space that I would like to exclude from the area measurement. I guess another way to put it would be to fill holes but only those below a certain size.
As I would like to later eliminate non-lung tissue (by splitting and then excluding the non-lung tissue) it would be preferable to not do the above by creating a mask as it will add the additional step of correlating it with a non-mask image.
The images are extracted from a whole slide scanner so file sizes range from about 50MB to 1GB and I have hundreds of images so processing time is a concern.