Hybrid Microdrive System with Recoverable Opto-Silicon Probe and Tetrode for Dual-Site High Density Recording in Freely Moving Mice

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This protocol describes the construction of a hybrid microdrive array that allows implantation of nine independently adjustable tetrodes and one adjustable opto-silicon probe in two brain regions in freely moving mice. Also demonstrated is a method for safely recovering and reusing the opto-silicon probe for multiple purposes.

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Osanai, H., Kitamura, T., Yamamoto, J. Hybrid Microdrive System with Recoverable Opto-Silicon Probe and Tetrode for Dual-Site High Density Recording in Freely Moving Mice. J. Vis. Exp. (150), e60028, doi:10.3791/60028 (2019).


Multi-regional neural recordings can provide crucial information to understanding fine-timescale interactions between multiple brain regions. However, conventional microdrive designs often only allow use of one type of electrode to record from single or multiple regions, limiting the yield of single-unit or depth profile recordings. It also often limits the ability to combine electrode recordings with optogenetic tools to target pathway and/or cell type specific activity. Presented here is a hybrid microdrive array for freely moving mice to optimize yield and a description of its fabrication and reuse of the microdrive array. The current design employs nine tetrodes and one opto-silicon probe implanted in two different brain areas simultaneously in freely moving mice. The tetrodes and the opto-silicon probe are independently adjustable along the dorsoventral axis in the brain to maximize the yield of unit and oscillatory activities. This microdrive array also incorporates a set-up for light, mediating optogenetic manipulation to investigate the regional- or cell type-specific responses and functions of long-range neural circuits. In addition, the opto-silicon probe can be safely recovered and reused after each experiment. Because the microdrive array consists of 3D-printed parts, the design of microdrives can be easily modified to accommodate various settings. First described is the design of the microdrive array and how to attach the optical fiber to a silicon probe for optogenetics experiments, followed by fabrication of the tetrode bundle and implantation of the array into a mouse brain. The recording of local field potentials and unit spiking combined with optogenetic stimulation also demonstrate feasibility of the microdrive array system in freely moving mice.


It is crucial to understand how neuronal activity supports cognitive process, such as learning and memory, by investigating how different brain regions dynamically interact with each other. To elucidate dynamics of the neural activity underlying cognitive tasks, large-scale extracellular electrophysiology has been conducted in freely moving animals with the aid of microdrive arrays1,2,3,4. In the past two decades, several types of microdrive array have been developed to implant electrodes into multiple brain regions for rats5,6,7,8 and mice9,10,11,12. Nonetheless, current microdrive designs generally do not allow for the use of multiple probe types, forcing researchers to choose a single electrode type with specific benefits and limitations. For example, tetrode arrays work well for densely populated brain regions such as the dorsal hippocampus CA11,13, while silicon probes give a better geometrical profile for studying anatomical connections14,15.

Tetrodes and silicon probes are often used for in vivo chronic recording, and each has its own advantages and disadvantages. Tetrodes have been proven to have significant advantages in better single unit isolation than single electrodes16,17, in addition to cost effectiveness and mechanical rigidity. They also provide higher yields of single unit activities when combined with microdrives8,18,19,20. It is essential to increase the number of simultaneously recorded neurons for understanding the function of neural circuits21. For example, large numbers of cells are needed to investigate small populations of functionally heterogeneous cell types such as time-related22 or reward coding23 cells. Much higher cell numbers are required to improve the decoding quality of spike sequences13,24,25.

Tetrodes, however, have a disadvantage in recording spatially distributed cells, such as in the cortex or thalamus. In contrast to tetrodes, silicon probes can provide spatial distribution and interaction of local field potentials (LFPs) and spiking activities within a local structure14,26. Multi-shank silicon probes further increase the number of recording sites and allow recording across single or neighboring structures27. However, such arrays are less flexible in the positioning of electrode sites compared to tetrodes. In addition, complex spike sorting algorithms are required in high-density probes to extract information about action potentials of neighboring channels to mirror the data acquired by tetrodes28,29,30. Hence, the overall yield of single units is often less than tetrodes. Moreover, silicon probes are disadvantageous due to their fragility and high cost. Thus, the choice of tetrodes vs. silicon probes depends on the aim of the recording, which is a question of whether obtaining a high yield of single-units or spatial profiling at the recording sites is prioritized.

In addition to recording neural activity, optogenetic manipulation has become one of the more powerful tools in neuroscience to examine how specific cell types and/or pathways contribute to neural circuit functions13,31,32,33. However, optogenetic experiments require additional consideration in microdrive array design to attach the fiber connector to stimulation light sources34,35,36. Often, connecting fiber-optics requires a relatively large force, which may lead to a mechanical shift of the probe in the brain. Therefore, it is not a trivial task to combine an implantable optical fiber to conventional microdrive arrays.

For the above reasons, researchers are required to optimize the selection of the type of electrode or to implant an optical fiber depending on the aim of the recording. For example tetrodes are used to achieve higher unit yield in hippocampus1,13, while silicon probes are used to investigate the laminar depth profile of cortical areas, such as the medial entorhinal cortex (MEC)37. Currently, microdrives for simultaneous implantation of tetrodes and silicon probes had been reported for rats5,11. However, it is extremely challenging to implant multiple tetrodes and silicon probes in mice because of the weight of the microdrives, limited space on the mouse head, and spatial requirements for designing the microdrive to employ different probes. Although it is possible to implant silicon probes without a microdrive, this procedure does not allow for adjustment of the probe and lowers the success rate of silicon-probe recovery12,38. Furthermore, optogenetic experiments require additional considerations in microdrive array design. This protocol demonstrates how to construct and implant a microdrive array for chronic recording in freely moving mice, which allows implantation of nine independently adjustable tetrodes and one adjustable opto-silicon probe. This microdrive array also facilitates optogenetic experiments and recovery of the silicon probe.

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All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Texas Southwestern Medical Center.

1. Preparations of microdrive array parts

  1. Print the microdrive array parts using a 3D printer using dental model resin (Figure 1A,B). Ensure that the thickness of individual 3D printed layers is less than 50 µm to keep the small holes on the printed parts clear and viable.
    NOTE: The microdrive array consists of five parts (Figure 1C): (1) the main body of the microdrive array, which includes nine microdrive-screws for tetrodes and one screw for a silicon-probe (Figure 1Ca-d). The coordination of the tetrode bundle and hole for the opto-silicon probe at the bottom depends on the target brain area’s coordinates (Figure 1Cd); (2) a shuttle to attach a silicon-probe or optrode (Figure 1Ce); (3) a probe electrical connecter mount to hold the silicon probe connecter (Figure 1Cf); (4) a fiber ferrule holder that clamps to the center part of the body to prevent undesired movements of the implanted opto-silicon probe when plugging/unplugging an optical fiber connector (Figure 1Cg); and (5) a shielding cone that provides physical and electrical shielding to the microdrive array for stable recording (Figure 1Ch). The total weight of the microdrive array is 5.9 g, including the shielding cone (Table 1). If holes are clogged in the printed parts, drill out the holes using drill bits: #76 for the inner holes and #68 for the outer holes for tetrode-microdrive screws, #71 for tetrode microdrive-screw supporter hole, and #77 for the holes for the guide-posts at the bottom of the body.
  2. Insertion of guide posts into the microdrive array body.
    1. Cut two 16 mm lengths of 26-Ga stainless steel wire. Gently sharpen the wire tips using a rotary grinder.
    2. Insert the wires into the bottom holes of the body (Figure 2A). Apply a small amount of cyanoacrylate glue at the bottom of the body to secure the guide posts.

2. Opto-silicon probe preparation

  1. Prepare the microdrive screw for a silicon-probe.
    NOTE: The microdrive screw for the silicon probe consists of a custom screw (300 µm pitch), supporting a support tube, and an L-shape tube (Figure 2B).
    1. Prepare the mold for the microdrive head (Figure 2C). To construct the mold, prepare the 3D-printed plastic pattern of the microdrive (Figure 2Ca). Then, pour liquid silicone gel after making a temporal wall by putting tapes around the pattern. Remove air bubbles by shaking gently, wait until it is cured, then remove the silicone-gel mold from the pattern (Figure 2Cb).
    2. Cut 18 mm and 9.5 mm lengths of 23 G stainless wire using a rotary grinder. Roughen the top 2–3 mm of the wires with a rotary grinder to enhance adhesion of the dental acrylic.
    3. Take one custom screw and apply small amount of silicon oil to reduce the friction with the dental acrylic. Set the wires and a custom-screw to the mold.
    4. Pour dental acrylic into the mold using a syringe to eliminate air bubbles around the wires and the screws. Air bubble contamination will make the microdrive fragile. Wait until the dental acrylic is fully cured, then take off the microdrive screws from the mold. Bend 6 mm of the longer wire tip to a 60° angle using pliers.
    5. Check the quality of the microdrive screws (e.g., cracks, air-bubbles, and friction) to rotate the screw. If there is high friction, rotate the screw until they become smooth using an electric screw driver with a customized driver tip, which couples with the microdrive screw.
    6. Install the microdrive screw into the microdrive array body to check whether it moves up and down smoothly by turning the screw. Threads for the screw are automatically created when inserting the screw into the hole of the body.
  2. Prepare the shuttle (Figure 3Aa).
    1. Cut two 5 mm lengths of polyetheretherketone (PEEK) tubing using sharp scissors. Align the tubes at both sides of the shuttle. Glue the tubes and shuttle using epoxy.
    2. Apply small amount of silicon oil on the guide posts. Check the quality of the shuttle by inserting onto the guide posts of the microdrive array body. Make sure the shuttle moves smoothly without excessive friction.
  3. Prepare an optorode (Figure 3Ab). This step can be skipped if an optogenetic experiment is not required.
    1. Cleave the optical fiber to 21 mm in length using a ruby cutter. Grind the fiber tip to make the tip flat and shiny.
    2. Gently place the optical fiber on the front side of the silicon-probe. The fiber tip is positioned 200–300 µm above the top of the electrode sites. Hold the fiber temporarily with transparent tape.
    3. Glue the optical fiber to the base of the silicon-probe using small amount of epoxy. Wait for at least 5 h until the epoxy is fully cured.
      NOTE: It is recommended to attach the optical fiber on the same side as the electrode sites. Attaching the fiber at the backside may prevent light from properly illuminating the recording sites.
  4. Attach the shuttle to the silicon probe (Figure 3Ac): apply a small amount of epoxy at the back of the silicon-probe’s base. Attach the bottom part of the shuttle to the silicon-probe’s base, and gently hold in position for 2–3 min to avoid formation of a gap between the shuttle and silicon-probe base during initial cure of the epoxy. Wait for at least 5 h until the epoxy is completely cured.
  5. Carefully insert the shuttle tubes onto the guide posts of the main body under the microscope (Figure 3B). During this procedure, hold the groove of the shuttle with fine tweezers.
  6. Insert the microdrive-screw into the screw hole by turning the screw. Engage the silicon probe and microdrive-screw by inserting the tip of the L-shape wire into the groove of the shuttle head (Figure 3C).
  7. Attach the probe electrical connecter holder to the microdrive array body (Figure 3D).
    1. Cut two #0 screws to 3.5 mm thread length. Grind the tips to remove burrs.
    2. Place the probe connecter holder on the body. Place the silicon probe electrical connector into the holder.
    3. Secure the silicon probe connector in the holder using epoxy, and be sure to not glue it to the microdrive array body to allow for the recovery procedure of the silicon probe. Insert the screws to hold the probe connecter holder.
  8. Attach the ferrule-holder to the opto-silicon probe and microdrive array body (Figure 3D).
    1. Cut two #0 screws to 6 mm thread length. Grind the tips to remove burrs.
    2. Grind the outside of two #0 machine screw nuts to make small hex nuts with 2.5–3.0 mm outer diameter to reduce the weight and space.
    3. Insert the screws into component A of the holder. Glue the screw heads using epoxy.
    4. Apply small amount of silicon grease to component A and B to reduce friction with the body. Insert component A into the body, then temporally hold using inverse tweezers.
    5. Place component B onto component A’s screws. Thread the customized nuts into the screws. Use pliers to tighten the nuts to secure the ferrule holder on the body.
    6. Insert the fiber ferrule into the groove of the fiber ferrule holder (component B). Ensure that the fiber ferrule is sticking 4–5 mm out from the holder.
    7. Apply small amount of epoxy between the ferrule and the holder groove. Wait until the epoxy is fully cured and check that the ferrule does not move. Check the shuttle and ferrule holder for smooth motion by loosening the nuts before turning the microdrive-screw.
    8. Check the working distance of the probe. Ensure that the probe tip completely retracts into the body when the ferrule-holder is at the top position while the shuttle tubes are still associated with the guide-posts. The maximum working distance is determined by the length of the silicone probe and the target brain region.
    9. If the microdrive-screw is loose, apply small amount of dental acrylic around the screw to add more threads for support. When it is cured, rotate the screw to check tightness and stability.

3. Tetrode preparation

NOTE: This procedure is similar to previously published articles8,19,20,39.

  1. Prepare the microdrive screws for the tetrode. The microdrive for a tetrode consists of a custom-machined screw and a 23 G tubing (Figure 2B). This procedure is similar to section 2.1.
  2. Make a bundle of 30 G stainless steel tubing that has a 5.5 mil wire inside. In this case, a total of nine 30 G tubing (eight recording tetrodes and one reference electrode) were used.
  3. Thread the 30 G bundle from the bottom of the drive body, and secure them with 20 G thin-walled tubing to the main body. Trim the bottom of the bundle with a rotary grinder to make the tip even and flush. Trim top part of the 30 G tubes with a rotary grinder so that the 30 G tube sticks out about 0.5 mm from the main body.
  4. Load 5.5 mil polyimide insulating tubes into the 30 G tubing. Prepare tetrode wires and load them into a 32-channel electric interface board (EIB). Check electrical connection with the impedance tester before final precision cut.
  5. Lower electrode tip impedance to 250–350 kΩ with gold plating solution. Fix all tetrodes with superglue.
  6. Fill excessive gap between polyimide tube and tetrode with mineral oil for sealing and lubrication. Route the ground wire to the EIB.
    NOTE: If necessary, the optical fiber can be integrated along tetrode wires12.

4. Attaching the shielding cone

  1. Paint silver conductive shielding paint on the inside of the printed cone. Place the microdrive array inside of the cone (Figure 3E).
  2. Cut two #0 screws to 3.5 mm thread length. Fasten the screws from the outside of the cone to hold the microdrive array in place.
  3. Apply silver paint around the screw head to electrically connect the shielding cone with electrical ground. Check the electrical connectivity between the ground wire and cone. Apply a small amount of epoxy between the microdrive array body and shielding cone to securely attach the body.
    NOTE: Another way to prepare the shielding cone is to use aluminum tape40 (Figure 3F). First, prepare the pattern paper for the shielding cone after sticking aluminum foil to the paper (Figure 3Fa). Then, roll the paper and attach it to the microdrive body using a small amount of cyanoacrylate glue (Figure 3Fb). The weight of this cone is 0.72 g and total weight of the microdrive array is reduced to 4.7 g (Table 1).

5. Implant surgery

NOTE: This procedure is modified from previously published articles18,39,41 for dual-site implantation. Ensure that the weight of the animal is over 25 g for the microdrive implant for faster recovery after the surgery.

  1. Preparation
    1. To prepare a ground screw, attach the silver wire to a skull screw and apply silver paint. Then, attach a gold pin to the opposite side of the wire using silver paint.
    2. Prepare the drive holding adapter to hold the microdrive array to a stereotactic device. Attach a male connecter to a stainless handle using epoxy. Make sure that alignment of the connecter and stainless handle is straight.
    3. In the case that histological confirmation is needed after recording, apply Di-I to the tetrodes or backside of the silicon-probe38.
    4. Lower the silicon-probe down to be desired depth. Loosen the nuts of the ferrule holder using pliers, lower the silicon-probe (opto-silicon probe) by turning the silicon-probe’s microdrive-screw, then fasten the nuts to secure the ferrule holder. When implanting tetrodes in hippocampal area CA1 and a silicon-probe in MEC, the distance between the tetrode cannula and silicon-probe’s tip is 3–4 mm.
  2. Set the anesthetized mouse (0.8%–1.5% isoflurane) in a stereotaxic device. The anesthetic condition of the mouse is confirmed by absence of the toe-pinch reflex. Apply clear ointment to the eyes to prevent drying. Cover the eyes with a piece of foil to protect from strong surgical light exposure.
  3. Disinfect the mouse’s scalp with iodine and isopropanol after shaving the fur. Make a 1.5–2.0 cm incision at the scalp using standard surgical scissors, and remove the tissue over the skull using cotton swabs after subcutaneously applying lidocaine.
  4. Align the mouse head with the stereotaxic tool. Ensure that the height difference between bregma and lambda is less than 100 μm. Determine the craniotomy location using an atlas and mark these locations with a sterilized pencil.
  5. Anchor the skull screws (0.8 mm diameter, 0.200 mm thread pitch) by rotating them 1.5 turns (0.3 mm) on the skull, using surgical tweezers and a screwdriver after drilling 8–11 holes in the skull using 0.5 mm drill bit.
    NOTE: 2–4 holes in the frontal skull, 2–3 holes in each side of the parietal skull, and 1–2 holes in the interparietal skull are suggested.
  6. Attach the ground screw to the hole by rotating it one turn (0.2 mm) after drilling a hole in the interparietal bone. Ensure that this hole does not penetrate through the bone into the brain case; otherwise, cerebellar signals will contaminate the recording. Check that the impedance is less than 20 kΩ at 1 kHz between the ground screw and skull screws using an impedance meter.
    NOTE: Larger impedance will cause the introduction of motion artifacts during recording.
  7. Perform the craniotomy at the marked locations. The dura can be left intact in mice.
  8. Connect the male pin of the ground screw and the microdrive array’s ground connector. Check connectivity using the impedance meter by measuring between the ground screw and shielding.
  9. Set the microdrive array to the adapter, set it to the stereotaxic device, and slowly lower the silicon probe until the desired depth. Ensure that the tetrode bundles are placed above the brain surface but still inside of the microdrive array when the silicon probe is inserted into the brain (Figure 4A).
  10. Carefully apply the silicon grease to seal the area of the silicon probe and the tetrode bundle (Figure 4B). Put a small amount of the silicon grease at the tip of a 20 G needle and apply the grease around the probes using the needle. Repeat until silicon grease completely covers the area around the probe so that dental acrylic does not flow onto or underneath the electrodes/probes. Be careful not to let the grease touch the electrode sites, otherwise it will dramatically increase the impedance of the recording sites.
  11. Apply dental acrylic to fix the microdrive array to the anchoring screws in the skull.
    NOTE: It is recommended to apply dental acrylic in three layers to avoid the excessive heat produced during curing of the acrylic.
  12. Remove the adapter from the microdrive array carefully. Inject 1 mL of PBS subcutaneously to prevent dehydration. Inject 5 mg/kg meloxicam subcutaneously as an analgesic treatment.
  13. Cover the silicon-probe connector by a piece of tape to prevent any dirt from getting inside of the electrical connections. Cover the microdrive array using a plastic paraffin film and tape it in place.
  14. Administer appropriate analgesic treatment for 3 days (e.g., subcutaneous injections of 2 mg/kg meloxicam once per day). Allow 3–5 days for recovery before starting the tetrode adjustment. The implanted mouse after the recovery period is shown in Figure 4C.

6. Recovering the silicon-probe (Figure 4D)

  1. Inject ketamine (75 mg/kg) and dexmedetomidine (1 mg/kg) anesthetics intraperitoneally and confirmed absence of the toe-pinch reflex. Fix the anesthetized mouse by directly perfusing 4% paraformaldehyde through the heart using a hood. Surgical methods for rodents are described previously42.
  2. Loosen the nuts of the ferrule holder using a plier. Then, carefully move it to the top of the body by turning the adjusting screw to fully retract the silicon-probe towards inside of the microdrive array body. Fasten the nuts to hold the probe at the top position.
  3. Take the mouse brain out from the bottom by cracking the skull from the side. The microdrive array is now separated from the animal.
  4. Completely remove the L-shaped microdrive-screw that drives the silicon-probe. Loosen and take out the nuts of the ferrule holder using pliers. Take out the component A of the ferrule holder.
  5. Unscrew the probe connector mount and detach from the drive body. Check that the probe connector mount can come off from the microdrive array body.
  6. Hold the top part of the shuttle with tweezers, then carefully slide the silicon-probe assembly out from the microdrive array.
  7. Clean the probe tip with contact lens cleaner (first with enzyme, then 3% hydrogen peroxide) for at least 1 day. Carefully wipe the electrode tip using isopropanol pads under the microscope. Keep the probe in a static-free storage box.
    NOTE: The shuttle and probe connector mount remain attached to the silicon probe and can be reused in the next implantation.
    NOTE: Some silicon probes are not tolerable with hydrogen peroxide. In this case, use the contact lens solution containing proteolytic enzyme only.
  8. To reuse the microdrive array body for the next surgery, remove the dental acrylic using a combination of fine-tip drills and nippers. Then, recover the skull-screws by immersing the removed dental acrylic into acetone. Note that the acetone will dissolve plastic parts of the microdrive array.
  9. Remove the epoxy between the microdrive body and shielding cone using a scalpel.
    NOTE: No additional parts need to be printed again for the next surgery if the microdrive is not broken.

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Representative Results

The microdrive array was constructed within 5 days. The timeline of microdrive preparation is described in Table 2. Using this microdrive, nine tetrodes and one silicon probe were implanted into the hippocampal CA1 and MEC of the mouse [21 week old/29 g body weight male pOxr1-Cre (C57BL/6 background)], respectively. This transgenic mouse expresses Cre in MEC layer III pyramidal neurons. The mouse was injected with 200 nL of AAV5-DIO-ChR2-YFP (titer: 7.7 x 1012 gc/mL) into the MEC 10 weeks before the electrode implant. LFPs were recorded using a low-pass filter (1-500 Hz), and spiking units were detected using a high-pass filter (0.8-5 kHz). Light stimulation (λ = 450 nm) was performed using a 1 ms pulse width at 10.6 mW intensity measured at the end of the fiber connector. The reference electrode for the tetrode recording was placed in the white matter using a dedicated tetrode wire. The reference for the silicon probe recording was set as the top channel of the probe.

After the tetrode adjustment, behavioral performance was tested on a linear track (Figure 5A) and in an open field (Figure 5B). In both experiments, the mouse explored freely for ~30 min (Figure 5Aa,b,c; Figure 5Ba,b,c). The electrophysiological signals were successfully recorded without severe motion-related noise throughout the recording session (Figure 5Ad,e; Figure 5Bd,e). Next, light stimulation was performed at the MEC to stimulate MEC layer III neurons that project to the CA143 (Figure 6A). Spontaneous spiking activities (Figure 6B,C) and LFPs (Figure 6D) were recorded from the tetrodes and silicon probe when the mouse was sleeping. LFPs recorded in the tetrodes showed large ripple activities, suggesting that all tetrodes were positioned in the vicinity of the CA1 pyramidal cell layer. Light-induced responsive activities were first observed in MEC, followed by in CA1 with 13-18 ms latency (Figure 6E).

Figure 1
Figure 1: Microdrive array overview. (A) A skeleton view of the microdrive array, from the tetrode side (a) and silicon-probe side (b). (B) A real image of the loaded microdrive array, viewed from the tetrode side (a) and from the silicon-probe side (b). The microdrive array is placed on the jig stage in panel (b). (C) Individual 3D-printed microdrive array parts. (a-d) The microdrive array body, viewed from four different angles (a: tetrode side view; b: silicon-probe side view; c: top view; d: bottom view). A magnified view of the dashed line in panel (c) is shown in Figure 2A. (e) The shuttle, which holds and allows adjusting of the silicon-probe. A silicon probe is attached at the dashed line in panel (e). (f) The probe-connecter holder, which holds a 32-channel silicon-probe connecter. (g) The fiber ferrule holder, which holds an optical fiber ferrule to prevent from the movement of the probe when plugging/unplugging the fiber connector with the light-source. This part consists of two components: [panel (g) and components A and B]. (h) The printed shielding cone, which provides physical and electrical shielding when painted with conductive material. The cone window allows the ability to see inside of the structure during microdrive array preparation, which is eventually covered by a piece of tape or 3D-printed material. Please click here to view a larger version of this figure.

Figure 2
Figure 2: Preparation of guide-posts and microdrive screws on the main body. (A) Guide post-preparation. (a) Magnified view of the microdrive array body shown in Figure 1Cc. (b) Guide post-insertion into the holes of the body. (B) The microdrive-screw designs. (a) The microdrive-screw for a silicon-probe, which consists of a 300 µm pitch custom screw, supporting tube, and L-shape tube. (b) The microdrive-screw for a tetrode, which consists of a 160 µm pitch custom screw and 30 G stainless guide tube. (C) Fabrication of the top piece of the microdrive-screws: (a) Preparation of 3D-printed patterns of the anti-mold for the microdrive-screw. The picture shows a pattern for the silicon-probe microdrive-screw. (b) The mold made using the anti-mold pattern (a) and silicon-rubber material. Assembled microdrive-screws are produced by inserting custom-screws and wires/tube, and pouring dental acrylic in each well. Inset: magnified view of the wells of the mold. Please click here to view a larger version of this figure.

Figure 3
Figure 3: Microdrive array assembly. (A) Preparation of an opto-silicon probe. (a) Attaching two plastic guide tubes to the shuttle. (b) Gluing the optical fiber to the silicon-probe. (c) Attaching the shuttle to the opto-silicon probe. In this picture, the bottom part of the shuttle (dashed line) is attached to the silicon-probe’s base [backside of (b)]. The shuttle and the silicon probe shank should be in parallel. (B) Loading the opto-silicon probe shuttle assembly into the guide-posts of the microdrive array body. (C) Relative position of the silicon-probe microdrive when the probe is completely retracted into the body (a) and when positioned at the lowest in the drive body (b). The L-shape wire is inserted into the groove on the shuttle. (D) An exploded view of the fiber ferrule holder and the probe connector mount. (E) Shielding cone attached. The conductive material is painted inside of the cone. (F) Alternative shielding cone using a paper and aluminum tape. (a) A pattern paper. (b) An attached alternative shielding cone, which reduces 1.1 g of weight compared to the 3D-printed version. Please click here to view a larger version of this figure.

Figure 4
Figure 4: Sealing the probes during surgery and recovery of the silicon probe. (A) The microdrive array and the mouse skull after craniotomy, before applying silicon-grease. The silicon-probe is inserted about 2mm into the brain at this time. (B) Applying silicon-grease around the silicon-probe and tetrode bundles to protect the probes from dental acrylic. (C) The chronically implanted mouse after the recovery period, when the mouse is walking (a), grooming (b), and when connected to the recording cable with the counter-balancing pulley system (c). (D) The recovered silicon probe, before (a) and after (b) immersion into the cleaning solution. The biological tissues in (a) are removed after the cleaning process (b). Please click here to view a larger version of this figure.

Figure 5
Figure 5: Examples of simultaneous tetrode/silicon-probe recording in the hippocampal CA1 and medial entorhinal cortex (MEC) from the behaving mouse. (A) Recording on the linear track. (a) The linear track used for the recoding. (b) Trajectories of the mouse exploration for ~30 min on the track. (c) Behavioral performance on the linear track. (d-e) Representative LFP recordings from the tetrode (d) and the silicon-probe (e). (B) Recording in the open field. (a) The open field chamber used for the recoding. (b) Trajectories of the mouse exploration for ~30 min in the chamber. (c) Behavioral performance in the open field. (d,e) Representative LFP recordings from the tetrode (d) and the silicon-probe (e). LED is attached to the head amplifier to record the positions of the mouse. The linear track and the open-field chamber are connected with the electrical ground to reduce electrostatic noise. Please click here to view a larger version of this figure.

Figure 6
Figure 6: Representative results of simultaneous recordings in the CA1 and MEC and optogenetic stimulation. (A) Expression of AAV5-DIO-ChR2-YFP after 4 weeks of injection. MEC layer III pyramidal neurons that project their axons from dorsal MEC to dorsal CA1. Dashed lines: ori, stratum oriens; pry, stratum pyramidale; rad, stratum radiatum; mol, stratum lacunosum moleculare. (B) Representative spike recording from one of the tetrodes. (a) 2D cluster projections of spikes recorded from the tetrode. (b) Examples of the average spike waveform of three clusters, which are indicated by dashed lines in (a). (C) Representative spike recording from one of the silicon-probe electrode sites. (a) 2D cluster projections of spike principal components. (b) Examples of the average spike waveform of three clusters. Spike clusters (pink and green) are separated from the noise clusters (blue). The clusters in (B,C) are calculated using KlustaKwik software. (D) Traces of spontaneous LFPs simultaneously recorded from the tetrodes in CA1 (a) and the silicon probe in MEC (b). Black arrows indicate the tetrode shown in (B) and silicon-probe electrode site shown in (C). (E) LFP responses to pulsed optical stimulation (10.6 mW, 1 ms; filled red arrowhead) from the tetrodes in CA1 (a) and silicon probe in MEC (b). Please click here to view a larger version of this figure.

grams/one number sum [gram]
main body 1.25 1 1.25
shuttle 0.04 1 0.04
probe connecter mount 0.19 1 0.19
fiber ferrule holder 0.1 1 0.1
shielding cone 1.82 1 1.82 (0.72)*
conductive paste 0.2 1 0.2
machine screw (#00, 2 mm), to hold EIB 0.05 2 0.1
machine screw (#0-80, 3.5 mm) 0.06 4 0.24
machine screw (#0-80, 6mm) 0.09 2 0.18
nut 0.03 2 0.06
microdrive (tetrode) 0.05 9 0.45
microdrive (silicon probe) 0.29 1 0.29
silicon probe 0.28 1 0.28
electric interface board 0.6 1 0.6
total 5.8 (4.7)*

Table 1: Individual weight of each microdrive array part. The total weight of the microdrive array was 5.9 g after fixing the protective cone with epoxy (*in the case of using an alternative shielding cone using a paper and aluminum tape).

procedures time
microdrive preparation
3D parts printing 1 day
optrode preparation
Prepare the mold for the microdrive head 1 day*
Microdrive head preparation 3 h
Attaching an optical fiber 3 h
Attaching a shuttle 3 h
tetrode preparation
Prepare the mold for the microdrive head 1 day*
Microdrive heads preparation 3 h
Loading tetrode wires 1 day
Attaching the shielding cone
Painting shielding paint overnight*
Attaching to the microdrive body 3 h
* these procedure can be conducted in parallel

Table 2: The timeline of the microdrive preparation. The 3D-parts printing, waiting for curing the silicone rubber/dental acrylic/epoxy, and loading the tetrode wires take the majority of the time of the microdrive array preparation, in total 4-5 days.

Supplementary Files: The supplementary files include 3D model data of five microdrive parts in both .sldprt and .stl format. The original 3D model files were created with the software Solidworks2003. Please click here to download this file.

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The protocol demonstrates how to construct and implant a hybrid microdrive array that allows recording of neural activities from two brain areas using independent adjustable tetrodes and a silicon-probe in freely behaving mice. It also demonstrates optogenetic experiments and the recovery of the silicon probe after experiments. While adjustable silicon probe33 or opto-silicon probe36 implantation are previously demonstrated in mice, this protocol has clear advantages in the simultaneous tetrode array and opto-silicon probe implantation to provide flexible choice of implanted probe types. The type of implanted probe can be switched depending on the aim of the experiment, such as multi-shank probes27,44 or ultra-density Neuropixels21,45. The coordination and angle of implantation7 can be easily modified at the 3D object design stage as needed. For example, dual-site or even triple-site recording is possible during learning tasks across memory-related brain structures, such as the hippocampus46, entorhinal cortex47, prefrontal cortex48, amygdala49, and cingulate cortex50.

There are several critical procedures for successful implant and recording. Due to the fragility of silicon-based probes, any mechanical vibrations or impacts to the microdrive array should be minimized during assembly. For example, opening the clogged holes using a drill should be finished before loading the silicon probe into the microdrive array. Also, it should be emphasized to carefully check the ground connection in each step during microdrive array construction and implant surgery to ensure stability of the recorded data. Unstable or high-impedance connections to the ground cause heavy noise and motion related artifacts during the recording session. For stable recordings, it is recommended to wait 1-2 weeks after the surgery to avoid electrode drift because the brain tissue is negatively affected by the implant surgery. However, signal quality on the silicon probe recovers after 1-2 weeks from the surgical trauma based on previous experience. It is recommended to use single-housing to prevent damage to the implanted microdrive array by other mice. For the optogenetic experiment, it is important to note that most silicon-probes induce photo-artifacts in response to light-stimulations51, while others are designed to minimize photo-artifacts52 (there are photo-artifact reduced silicon-probes that are commercially available).

The weight of the microdrive array (5.9 g) is heavier than the typical microdrives described in previous articles12,53, mainly due to the microdrive array body (~21% of the total weight), shielding cone (~31%), and metal parts (screws and nuts: ~22%). It is recommended to use mice with weights of over 25 g (~2-3 months old for C57BL/6 mice54,55) for implant surgery, because mice with adequate body weights tend to recover earlier. For this reason, this microdrive array may be not the best solution for juvenile mice. While devices that are 5%-10% of the mouse’s bodyweight are often guided to be tolerated for implants12,56 (although there is no supporting published data for this57), this microdrive array weighs ~24% of the bodyweight of 25 g mice (~19% when using the alternative cone described below).

However, the implanted adult mice were able to freely move around and jump around in the home cages. Mice implanted with a similar microdrive array weight (~4.5 g) have previously been shown to perform the behavioral task (linear maze task) even under food restriction13,17. The disadvantage of weight is not a problem during recording, as a counterweight balancing system18,34,58 or headpost system59 will support the microdrive array. In addition, the total weight of the microdrive array can be reduced by lowering the height or reducing the thickness of the shielding cone and modifying the design to utilize smaller screws.

Using the current 3D printing material, the thickness of the shielding cone can be reduced up to ~0.3 mm (from the current thickness of ~0.6 mm). The cone height can be reduced ~5 mm as long as the tetrode wires can still be covered. Exposure of the tetrode wires will result in breakage of the wires and failure of the long-term recording. Alternatively, preparation of the shielding cone using paper and aluminum tape can reduce the cone weight to ~0.7 g (~15% of total weight; reduced 20% from the total weight of the original microdrive array); although, these are a tradeoff with the physical strength. In addition, the size of the microdrive (current shielding cone: 4.2 x 4.0 x 2.6 cm = major axis x minor axis x height) can be an obstacle to food and water access if they are provided from the top of the animal cage. As long as they are provided on the cage floor or from the sidewall, the microdrive does not disturb natural behaviors of mice, such as eating, drinking, grooming, rearing, or nesting60.

In conclusion, this microdrive protocol provides researchers with flexible choices for recording from multiple brain areas in freely moving mice for understanding the dynamics and functions of long-ranging neural circuits.

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The authors have nothing to disclose.


This work was supported in part by Japan Society for the Promotion of Science Overseas Research Fellowships (HO), Endowed Scholar Program (TK), Human Frontier Science Program (TK), Brain Research Foundation (TK), Faculty Science and Technology Acquisition and Retention Program (TK), Brain & Behavior Research Foundation (TK), and by The Sumitomo Foundation Research Grant (JY), NARSAD Young Investigator Research Grant (JY). We thank W. Marks for valuable comments and suggestions during the preparation of the manuscript.


Name Company Catalog Number Comments
#00-90 screw J.I. Morris #00-90-1/8 EIB screws
#0-80 nut Small Parts B00DGB7CT2 brass nut for holding fiber ferrule holder
#0-80 screw Small Parts B000FMZ57G brass machine screw for probe connector mount, fiber ferrule holder, and shielding cone
22 Ga polyetheretherketone tubes Small Parts SLPT-22-24 for attaching to the shuttle, 0.025 inches inner diameter
23 Ga stainless tubing Small Parts HTX-23R for tetrode
23 Ga stainless wire Small Parts HTX-23R-24-10 for L-shape/support wire
26 Ga stainless wire Small Parts GWX-0200 for guide-posts
30 Ga stainless wire Small Parts HTX-30R for tetrode
3-D CAD software package Dassault Systèmes SolidWorks 2003
3D printer FormLab Form2
5.5mil polyimide insulating tubes HPC Medical 72113900001-012
aluminum foil tape Tyco Tyco Adhesives 617022 Aluminum Foil Tape for the alternative shielding cone
conductive paste YSHIELD HSF54 for shielding cone
customized screws for silicon-probe microdrive AMT UNM1.25-HalfMoon half-moon stainless screw, 1.5 mm diameter, 300 µm thread pitch
customized screws for tetrode microdrive AMT Yamamoto_0000-160_9mm slotted stainless screw, 0.5 mm diameter, 160 µm thread pitch, custom-made to order for our design
dental acrylic Stoelting 51459
dental model resin FormLab RS-F2-DMBE-02
Dremel rotary tool Dremel model 800 a grinder
drill bit Fine Science Tool 19007-05
electric interface board Neuralynx EIB-36-Narrow
epoxy Devcon GLU-735.90 5 minutes epoxy
eye ointment Dechra Puralube Ophthalmic Ointment to prevent mice eyes from drying during surgery
fiber polishing sheet Thorlabs LFG5P for polishing the optical fiber
fine tweezers Protech International 15-368 for loading/recovering the silicon probe
gold pins Neuralynx EIB Pins Small
ground wire A-M Systems 781500 0.010 inch bare silver wire
headstage preamp Neuralynx HS-36
impedance meter BAK electronics Model IMP-2 1 kHz testing frequency
mineral oil ZONA 36-105 for lubricating screws and wires
optical fiber Doric MFC_200/260-0.22_50mm_ZF1.25(G)_FLT
Recording system Neuralynx Digital Lynx 4SX
ruby fiber scribe Thorlabs S90R for cleaving the optical fiber
silicon grease Fine Science Tool 29051-45
silicon probe Neuronexus A1x32-Edge-5mm-20-177 Fig. 3, 4A, 4B, 5
silicon probe Neuronexus A1x32-6mm-50-177 Fig. 4C
silicon probe washing solution Alcon AL10078844 contact lens cleaner
silicone lubber Smooth-On Dragon Skin 10 FAST for preparation of microdrive mold
silver paint GC electronic 22-023 silver print II coating, used for ground wires
skull screw Otto Frei 2647-10AC 0.8 mm diameter, 0.200 mm thread pitch
standard surgical scissors ROBOZ RS-5880
stereotaxic apparatus Kopf Model 942
super glue Loctite LOC230992 for applying to guide-posts
surgical tweezers ROBOZ RS-5135
Tetrode Twister Jun Yamamoto TT-01
tetrode wires Sandvik PX000004



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