Imobiliser prolem

Hello, Have a 97 300 TDI Disco. Have just spent last few weeeks changing the engine. Have got to the point of turning the key, but all I get is a clicking noise from the air con compressor. No dash lights just the red led flashing above the key. After a few mins the dash lights come on, but I cant get the starter to turn. I think the imobiliser is stopping the engine from turning. The car has been left for a few weeks with the battery dissconnected.
Is there a sequence to reset the imobiliser?
Grateful for any help.
Thanks
Chris Cowell