Ok...we have always used the entire slurry / yeast cake in the cone. It is nearly impossible to discriminate between the middle, top or bottom of the cake. It’s evenly distributed on the sides of the cone.
I am assuming that you do not have a valve part of the way up the cone from which to harvest yeast. If you do not have a harvesting valve and the conical is not too tall, you can crop from the top of cone. You have to determine the volume of the yeast cake. Here is the formula for the volume of a cone:
volume = 3.14 * radius^2 * (height / 3), where the symbol "^" denotes raised to the power of
The radius here is the diameter at that top of the cake divided by 2 because the cone is inverted. Let's say the diameter of the cone at the top of the cake is 4" and the height cake is 4".
radius = diameter / 2
volume = 3.14 * 2^2 * (4 / 3) = 3.14 * 4 * 1.33 = 16.7 cubic inches
The formula for cubic inches to milliliters conversion is: mL = cubic inches / 0.061024 = ~274 ml
We could divide the cake into thirds, but that is not how yeast settles out of suspension. If you have ever used a carboy, then you know that about a fifth of the sediment is break and particulate matter. We can assume that the next fifth or so is early flocculating and dead yeast cells. That leaves us with three fifths of the contents left to crop. However, the topmost layer consists of cells that have lost or losing their ability to flocculate. We do not want these yeast cells. A wise thing to do is to carefully remove and discard the top-most one fifth of the of the sediment. In this case, we want to skim 274 / 5 = 55ml from the top of the cone. We can then take our crop from the next two fifths, which is 110ml. The last two fifths is discarded. This cropping technique is far from perfect, but it should yield the best cells. One does not want to repitch the dead and early flocculating cells or the break. Because if you are repitching everything, the percentage of dead cells will increase with every repitch. Avoiding repitching the late flocculating yeast cells will should keep the culture from getting "powdery."
By the way, if you take your cone height and radius measurements in centimeters and use the volume of a cone formula to calculate cubic centimeters, one cubic centimeter (CC) equals one milliliter. That is why you see some syringes with CC instead mL markings.