Focusing on your puppy being calm in the crate lets you create a list of ways to achieve this goal. I will help you get started with this list. It is up to you to expand on this list and follow through.

1. Help your puppy develop a positive association with the crate by feeding them their meals there. Also, playing games with your puppy, going into the crate to fetch a toy or treat, and calling them out of the crate playfully and happily will allow them to associate fun and good things with the crate. 
2. Help your puppy learn to relax in the crate and that it’s not a torture device. Try putting the crate in a location where the puppy can see you. Try moving it to the living room if they cry or bark with the crate in the bedroom. Explore your options and see what works best. Place a bully stick, Lickimat, or stuffed Kong in their crate with them.
3. Help your puppy learn that it’s not the end of the world when you leave. If your puppy is very attached to you and can’t leave the house without them crying in the crate, you will have to start with a very short duration of 30-60 seconds and build up from there.  Once you get to the puppy being calm for 10-15 minutes, you should be OK.
4. Help your puppy desensitize to departure cues, such as the sound of the front door closing or you grabbing your keys to leave. This is the hardest part. If you are unsuccessful on your own, you should consider hiring a CSAT (Certified Separation Anxiety Trainer) to help you. This is usually done virtually so you can work with any CSAT anywhere in the world. 

These are just a few things you can do to help your puppy not bark or cry in the crate. Here is a great article from the ASPCA about separation anxiety.  This is not my expertise. I am only here to pass on some useful resources to you.

https://www.aspca.org/pet-care/dog-care/common-dog-behavior-issues/separation-anxiety

Purchase "The Business of Dog Training" on Amazon

RESOURCES:
Podcast Website: http://puppytalkpodcast.com
Sponsor Website: http://www.topgundogtraining.com
Dale's books: https://www.amazon.com/author/dalebuchanan