If the seeds are not floating in liquid from the tomato, add up to a cup of water to help separate the seeds from the pulp. Then set the bowl of tomato seeds and pulp in a warm, out of the way spot. You will need to allow 2-4 days for the fermentation to take place. As it does so, the mixture is going to begin to smell awful, so store the bowl where you won't pass by frequently.
If you have glass jars available, they make a good container for fermenting tomato seeds.
The extra space at the top of the jar controls some of the odor and the clear sides let you keep tabs on what is happening. Covering the top of the jar with cheesecloth or paper towel will keep fruit flies out and also diminish the spread of the unpleasant odor.
Remember to label each variety!
Fermentation is Complete
What you eventually want to see is a layer of mold on top of your seeds & pulp. The process is done when bubbles start rising from the mixture or when the entire bowl is covered with mold. Don't leave the seeds fermenting past this stage or they may begin to germinate.
Checking the Seeds in the Jar
It is harder to see the layer of mold through the glass jar, but you can generally tell the fermentation is complete when the seeds settle to the bottom of the jar in a watery liquid and the thicker pulp and mold sit on top of them.
Getting the Tomato Seeds Ready to Save
Finally you can remove and dispose of the mold covering. Lifting it before rinsing the seeds will make rinsing easier, but it's not necessary. You can add some water to the jar or bowl and stir or shake vigorously. The good seeds will settle to the bottom, allowing you to drain off the excess first.
Cleaning Your Fermented Tomato Seeds
Strain the seed mixture into a colander and rinse the seeds well under running water. Try to remove any remaining pulp bits and mold, so that only clean seeds remain.
Drying Tomato Seeds
Spread the seeds onto either a paper plate or glass dish, to dry. Don't use paper or paper towels or the seeds will stick to them and be difficult to remove. Set them in a warm, dry spot and allow to dry completely. Shake them on the plate daily to make sure they don't clump and that they dry evenly. Don't try to speed the process by using heat.
Storing and Saving Tomato Seeds
Once the seeds are thoroughly dry, you can store them in an air tight container, in a cool, dry place. The envelop shown here will be placed inside a canning jar. Remember to label and date your seeds!