soft agar colony counting - (Aug/01/2007 )

Hi,
I'm doing soft agar assay but I would like your advice how to count colonies at the very end.It is really hard to distinguish between dead/fragmented or splashed cells and actual colonies. I want to use dye that 'will see' difference in dead or alive cells so I thought about trypan blue. I know some people used also 0.4% crystal violet to count colonies. What do you suggest? Thanks in advance

what type of cells are you counting?

You could use a live-dead assay with fluorescein diacetate or Calcein-AM and PI. There's a protocol here that might be useful for you. I've used it to estimate colony growth in alginate hydrogel beads.