An 8-cm fiber is attached to a micromanipulator and ∼ 5 mm of the end is inserted into the acid for 15- to 30-min periods, until the desired 5–20 μm diameter is achieved (Fig. 1A). After rinsing in distilled water, the tip of the tapered end is cut with a diamond knife to provide a sharp clean edge while the non-etched end of the fiber is glued into a connector (LC type, Thorlabs no. 86024-5500) and polished following standard

procedures (as described in ‘Fiber polishing notes’, Thorlabs no. FN96A). The next step is to place the optical fiber on the shank of the silicon probe. This procedure is carried out with the help of micromanipulators and under microscopic vision. The silicon probe is placed horizontally and the fiber is positioned with a slight angle (15–20°) with the etched tip touching the shank at the desired distance Epacadostat from the recording sites. Then the remaining part of the fiber is pushed high throughput screening down with a piece of metal microtube so that it lies parallel to the surface of the shank (Fig. 1B). Once the fiber is in place, ultraviolet (UV) light-curable glue (Thorlabs no. NOA61) is applied by hand to the fiber and shank using a single bristle of a cotton swab. After successful application, UV light (Thorlabs no. CS410) is applied for 5 min. This procedure can be done in multiple steps by repeating

the process of pushing and gluing the fiber gradually upwards along the shank. Finally, the non-etched portion of the fiber is glued to the bonding area of the probe to provide secure connection. To avoid breakage of the fiber during handling and implantation, the connector end of the fiber and the probe base are interconnected with a metallic bar or/and dental cement (Fig. 2A). We made different designs of integrated fiber-based optoelectronic silicon devices to address different sets of questions (Fig. 2). Either one or four shanks were equipped with optical fibers, and the distance between the fiber tip and the recording

sites varied from 100 to 300 μm, depending on the desired volume of stimulated tissue. For experiments requiring the stimulation of neurons located below the recording sites only, an extra optical fiber was glued at the back of the shanks and protruded 100 μm below the shank tip (Fig. 2C). To maintain minimal shank thickness (15 μm) and guide the placement of the optical fibers, long 12-μm-deep grooves were etched at the back of the shanks Glycogen branching enzyme using a solid-state YAG laser-based laser micromachining system (LaserMill; New Wave Research, Inc., Freemont, CA, USA). Following the laser cut, the silicon grooves were fine polished at the very end of the shanks by chemically assisted focused gallium ion beam milling using a dual beam Focus ion beam/scanning electron microscope workstation (FEI no. DB-820). Liquid metal ion source-based gallium beam (30 kV acceleration) current of 150 pA at the sample surface was assisted by xenon difluoride (XeF2) gas for chemically enhanced silicon etching of the shank substrate.