Stephen's repetition of "coloured signs" after the phrase "Signatures of all things" in the previous sentence might indicate a continuing meditation on the thoughts of Jakob Boehme, but Gifford hears in this phrase an allusion to the comparably idealistic thoughts of the Anglo-Irish philosopher George Berkeley. Whether or not Stephen can be shown to be pondering Berkeley at the beginning of Proteus, he is certainly doing so near the end of the episode when he thinks of "the good bishop of Cloyne" (Berkeley was a bishop in the Church of Ireland) reading the world as if it is a sacred text.
Unlike the traditionally Christian Boehme (1575-1624), who lived several generations before him, Berkeley (1685-1753) espoused an idealism which needed to respond to the subject-object dualism of Descartes (1596-1650) and the empiricism of philosophers like John Locke (1632-1704). For Berkeley, ideal reality had to be defined in terms of the human subject who perceived materialistic phenomena, rather than simply in terms of the divine being who created them. His response was to argue that the things we think we perceive cannot be shown to be things at all, but only conditions in the mind of the perceiver. When a human subject thinks that he sees a material object, all that he in fact sees are light and color (hence Stephen's "coloured signs"). What Berkeley called the "immaterialism" of this view might readily be reconciled with the mystical transcendentalism of a thinker such as Boehme, producing "thought through my eyes."
Near the end of Proteus Stephen continues his meditation on reading the world as if it is a text full of written signs, rather than a space full of material objects. He sees the objects of his sight as swatches of color on a flat perceptual canvas that thought (mis)interprets as three-dimensional space: "Coloured on a flat: yes, that's right. Flat I see, then think distance, near, far, flat I see, east, back." Gifford helpfully glosses a sentence of Berkeley's, "Vision is the Language of the Author of Nature," as meaning that "the visible world is like a screen with signs on it, a screen that God presents to be read and thought rather than seen."
Working with this idea of flat mental space, Stephen imagines that Berkeley "took the veil of the temple out of his shovel hat: veil of space with coloured emblems hatched on its field." A veil is flat, and the veil of the temple is a sacred screen separating the holy of holies from the outside world, as Gifford observes in reading Exodus 26:31-35. The good bishop pulled this sacred veil out of his 18th century hat, i.e. he generated from his own mind a revolutionary understanding of perception as a window not onto an external world of material bodies, but onto the mental world of ideal realities.