Butter a 1 1/2 quart baking dish. Place bread cubes in bottom of dish in a single layer.
Heat olive oil in a large skillet over medium-high heat. Add onion to skilet and saute until translucent, 3-4 minutes. Add spinach and garlic to skillet. Saute another 3-4 minutes, or until spinach wilts. Remove from heat and set aside.
Whisk together eggs, thyme, salt, and pepper in a medium bowl. Stir in spinach mixture and chopped tomato. Pour egg mixture over bread in baking dish and sprinkle with cheese.
Refrigerate, covered, overnight. In the morning, remove dish from refrigerator and allow to stand for 30 at room temperature.
Preheat oven 375.
Bake strata for 25 minutes or until set. Allow to stand for 10 minutes.