By and with

By (doer or agent); with (instrument or means)

Examples:

He was punished by the teacher with a stick

She was murdered by her husband with a sword

He has a great influence on the headmaster

He has promised to comply with my request

He was killed by the robber with a Hatcher

He knows you by sight

Eggs are sold by dozens, apples by seers

I cannot put up with such conduct

A wise man profits from the experience

He quarrelled with me over a trifle