I harvested yeast from my primary fermenter and followed all the steps to wash it. When I looked in the fridge I noticed a darker layer in between two heathy, clean yeast layers. The bottom yeast layer is thicker so I'd like to keep the whole cake. Is that okay? Can I still store it, or should I use it right away? Also, if I can use it, should I use a specific size starter for a 5.5 gal. batch? I've only made starters for packs and vile yeast. This is my first harvested strain. Is there a difference in starter size?
If you're making a starter for it, you could split it between a couple batches with the idea that you will be do a starter for each. mrmalty.com has a yeast re-pitch section which is handy when using a yeast cake (slurry), but I believe that is assuming it has not been washed. So iirc, you will want to decrease the "trub" percentage to what you assume is the healthy yeast (the yeast on the top of the dark layer).
If you use a bucket for fermentation get a nilon paint strainer to put over your bucket when you poor your wort in. This will decrease your trub.
I often start my washed yeast with a healthy portion of trub to ensure that I get all or most of the yeast available. I haven't found that a small amount of trub (up to 50cc) affects my starter or my beer. Your starter size will depend on batch size and OG. My rule of thumb: for 5 gal. batches below OG 1.050 is 1 cup of DME in 1 litre of water. For OG above 1.050 (rare for me) I step the starter up one time with a 1/2 cup of DME. 1 cup of DME is about 100g of DME.
How many times did you wash the yeast? I typically do it 2-3 times and haven't really had any trub left over, really helps it keep longer.
I think yeast washing is overrated. I brew in a bucket and after I transfer from the fermenter to the bottling bucket I just stir the last bit of beer left in the fermenter into the trub then scoop 2-3 of cups of that mixture into a clean container and store in the fridge. If everything is sanitary, the yeast/trub should keep for weeks or months, and I've never had to create a starter from it to get vigorous ferments. A couple of extra cups of trub in a 5 gallon batch isn't really a big deal.
I noticed I let my wash sit too long and poured too much. After watching the Chop and Brew Episode below I was able to clean up my yeast wash much more. I actually took it from a jar and diluted it in a 3 gallon carboy and then followed the rest of their steps, it worked nicely. I had a ton of hops and what have yous in there.