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I have harvested seeds from a huge squash I grew. I put them i water for a few days. When I now pulled them out to dry them for storage, I see that some have just started sprouting already (the shell is open and the root is visible, up to about 3mm). Can I save these?

I live at 60 deg N, so have to wait until spring to plant anything outside, and I certainly don't have enough indoor space and light for big squash plant(s).

What is my best alternative - just dry them? store in fridge? underwater? can I freeze them? plant them and somehow slow down growth?

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I'd save the non-sprouted. Three days is a long wash, but you might get lucky come Spring. I've never met a seed that sprouted twice, excepting chard, and those are aggregates of seeds. No such luck with squash.

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After germination, a seed has broken dormancy and is now a living plant, so you can't save a seed that's germinated.

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As you can not save the seed, see the other answers, plant it.
Keep the plant in a low temperature but above freezing environment. If you have an outside area which will be free of freezing, use that. Otherwise a shed or area of the house that is not heated (much) as long as it is free of freezing.
Water lightly and allow to drain well, so the roots are not sitting in a wet mush.

I do not know if it works with squash but I have seen a TV gardener do it with several different kind of plants. And as you otherwise have to ditch the seeds, it is worth trying. It will give you a faster start in spring, so for some plants it is done on purpose.

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