Individual trays were embedded with a hole roughly 2.45 cm
You don't use the word 'embedded' with a hole. When we say something is 'embedded', it is enclosed or surrounded by something else.
Individual trays were each provided with a hole, roughly 2.45 cm in diameter.
Individual trays had a hole each, 2.45 cm in diameter.
Individual trays were each drilled with a hole, 2.45 cm in diameter.
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