No worries. I always collect in this fashion. You can proceed in one of two ways. 1) Pour most of the beer that stratifies on top of the yeast away then give what remains a good swirl and pitch or, 2) Swirl all contents and pitch. I also pitch cold, direct from my fridge. I found no reason to let it warm to ambient temps especially if you are making a lager. That is based on my brewing experience only. Another thing you may want to keep in mind if you are not already aware is that when storing collected yeast in your fridge, leave the lid loose so co2 doesn't build up pressure. It may cause autolysis when stored for longer periods. Again, just my experience.
Cheers!