As per Des's deleted post (I'll yield to them if they come back) this could be Monster Allergy, a 2005 animated adaptation of the comic book of the same name.
The series follows 12-year-old Ezekiel Zick (called Zick) who suffers from various allergies and has the ability to see the invisible monsters that live among us. Along with help of his best friend, Elena Potato and his talking cat, Timothy, Zick hopes to hone his powers to one day become a Monster Tamer just like his dad, Zobedja Zick.
They place the monsters in "Taming Boxes" like the following:
I don't believe there's a scientist character they interact with per se, but Zick's mother, Greta Barrymore, is a Keeper. That might be who you're thinking of.