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The gel can harbor bacteria when you're trying to save tomato seeds. Therefore, it's best remove the seeds from the gel before saving the seeds. The easiest way is to pick the seed out of the gel with the tip of a butter knife before moving on to drying. Another option is allowing the seeds to ferment. Basically, you just let the seeds sit on the counter somewhere in their own juices for a day or so. Place them in a strainer, and the gel should wash off. You may need to rinse them more than once. Don't save any seeds that float. The fermentation method will generally allow you to keep seeds longer, up to 5 years, but you can use the knife method to keep seeds for a year or two. Leave the seeds on a paper plate, part of a paper towel, or a coffee filter. They need to be spaced an inch or two apart. In fact, you can even plant the paper towels or coffee filters next spring, as they are biodegradable. It's best to only use the paper plate for the fermentation method, as then the seeds don't need as much help drying. The seeds can take up to a week or two to dry. They should be crackly when the are dry. That is, if you try to fold one, it should crack not bend. Make sure they aren't in the sun. Just keep them in a corner of your house at room temperature. If your area is particularly humid, it may take them longer to dry. Once the seeds are dry, you can place them in an airtight container or even an envelope. If you used coffee filters or paper towels, just fold them up with the seeds, and put them in the container. With the paper plates, you can dump the seeds into the container. Make sure to label it with the tomato variety and the date of when you saved them seeds. Store the seeds in a cool, dry place.
Remove the seeds from the gel. Spread the seeds out to dry. Let them dry. Save them for later.