LCA acknowledges funding from an NDSEG fellowship, the NSF GRFP, and the Friends of the McGovern Institute. EP acknowledges funding the Harry and Eunice Nohara UROP Fund, the MIT Class of 1995 UROP Fund, and the MIT UROP Fund. ESB acknowledges funding from NIH 2R44NS070453-03A1, the IET Harvey Prize, and the New York Stem Cell Foundation-Robertson Award. RD acknowledges funding from NIH EY017292. Michael Williams helped the team to organize and gather supplies prior to filming.

Note: All animal procedures were in accordance with the NIH guidelines and were approved by the Massachusetts Institute of Technology Committee on Animal Care.
1. Illuminator Fabrication
<ol>
	<li>Use a pair of sharp shears to cut a section of 250 &#181;m diameter plastic optical fiber that is at least 10 cm longer than the desired total illuminator length.</li>
	<li>Remove 15 - 20 cm of polyethylene jacket from one end of the plastic optical fiber using a 22 gauge wire stripper.</li>
	<li>Secure the distal most 3 - 5 cm of the stripped end of the fiber in a table vise clamp.</li>
	<li>Hold the jacketed end of the fiber taut in one hand with a constant steady pull. The fiber should be parallel to the floor, perpendicular to the vice. Maintain this constant tension on the fiber throughout heating and cooling (Steps 1.5 and 1.6 below) so that the fiber remains straight and taut as it thins.</li>
	<li>Using the lowest setting of a dual temperature heat gun (570/1,000 &#176;F,), heat the stripped section of the fiber until it is thinned to a diameter of 60 - 100 &#956;m, or about the diameter of a human hair.</li>
	<li>Maintain the constant tension on the fiber while allowing the fiber to cool. Failure to maintain tension may cause the fiber to curl.</li>
	<li>Confirm the diameter of the thinned tip under a dissecting microscope. Alternately, one may use calipers instead.
	<ol>
		<li>If the fiber is not thin enough, repeat steps 1.4 through 1.6 as needed to achieve the desired tip diameter.</li>
		<li>Optional if re-pulling, put a small mark at the narrowest portion of the fiber if it will be heated again so that the center of the heat gun targets the narrowest portion of the fiber.</li>
		<li>If the fiber is too thin, start over.</li>
	</ol>
	</li>
	<li>Once the fiber has full cooled and the desired diameter has been achieved, pinch the fiber 3 cm from the narrowest point on either side. With a quick, sharp pull along the axis of the fiber, separate the sides to create a tapered tip.</li>
	<li>Examine the tapered tip under a low power (e.g., 4X) on dissection microscope. If the tip is forked or curled (Figure 1f), discard the fiber.</li>
	<li>Prepare to etch the tapered tip by placing a piece of lab tape near the end of the tip, leaving the last 5 mm exposed. The tape protects the fiber from etching above the desired length of light emission. This tip length was selected based on thickness of primate cortex in the target region. A longer or shorter length could be exposed depending on the desired length of illumination. If a different etch tip length is desired, the edge of the lab tape can be moved closer to or farther from the tapered tip.</li>
	<li>Fold a small (~1 inch x 2 inch) square of 5 &#956;m silicon carbide lapping sheet over between the thumb and forefinger. Place the tip of the fiber between the two sides of the lapping sheet and gently etch the fiber using small circular motions, as if rolling a BB between the thumb and forefinger. Frequently rotate the fiber so that all sides are etched evenly. The fiber tip will appear &#8220;roughened&#8221; to the naked eye in areas that have been etched, while un-etched areas typically appear smooth.</li>
	<li>Repeat step 1.11 with a 3 &#956;m aluminum oxide lapping sheet.</li>
	<li>Affix a connector on the end of the illuminator opposite to the etched tip. This allows the illuminator to connect to an optical cable or laser. 
	Note: This method differs from the preferred method for fixing glass / silica optical fibers in ferrules. Because the metal ferrule is harder than the plastic optical fiber, polishing the fiber and ferrule as a unit after gluing can damage the plastic optical fiber as tiny shards of metal produced during the polishing process can embed themselves in flat-cleaved fiber.
	<ol>
		<li>Remove about 5 mm of the polyethylene jacket from the opposite end of the illuminator using a 22 gauge wire stripper.</li>
		<li>Cut the opposite end flat with a hot knife to smooth the surface.</li>
		<li>Polish the opposite end flat with successively finer lapping sheets: 5 &#181;m, 3 &#956;m, 1 &#956;m and 0.3 &#181;m.</li>
		<li>Insert the flat opposite end into a 260 &#181;m inner diameter stainless steel ferrule until it is flush with the end of the ferrule.</li>
		<li>Visually confirm that the opposite end is smoothly and evenly polished with a fiber microscope.</li>
		<li>Remove the fiber from the ferrule and tape the ferrule vertically on the edge of a table with the fiber pointing down.</li>
		<li>Fill a 1 mL syringe with plastic epoxy and attach a blunt 18 gauge needle to the syringe.</li>
		<li>Use the needle to apply epoxy down into the ferrule. Fill the ferrule completely with epoxy.</li>
		<li>Insert the fiber into the ferrule.</li>
		<li>Wipe any excess epoxy from polished surface of the fiber with a wet lint-free wipe prior to drying if needed. Otherwise, excess epoxy can be removed after 12 - 24 h.</li>
		<li>Store the fiber gently until calibration and place a dust cap over the ferrule.</li>
	</ol>
	</li>
</ol>
2. Illuminator Calibration and Quality Control
Note: These methods for calibration assess for light output non-linearity at different distances from the tip of the fiber. Uneven light distribution typically results from a &#8220;bumpy&#8221; or &#8220;wavy&#8221; taper.
<ol>
	<li>Create a light shielding diaphragm for the top of the integrating sphere using light absorbing foil (Figure 2). 
	Note: Wear gloves whenever handling light absorbing foil to prevent skin oils from creating light reflecting smudges.
	<ol>
		<li>Fold a 2&#8221; by 4&#8221; piece of light absorbing foil over on itself to form a 2&#8221; x 2&#8221; square. &#160;An alternative method is to cut a 2&#8221; x 2&#8221; square with one light absorbing side and one light reflecting side (i.e., a side of standard aluminum foil); however, the fold-over method is safer because it provides a dull edge for handling the diaphragm in the next step.&#160;</li>
		<li>Fold lab tape or electrical tape along the edges of the square to bind the non-folded edges. This both holds the sides together and protects against cuts from sharp edges.</li>
		<li>Puncture a hole in the center of the square using a 26 gauge needle.</li>
		<li>Remove the large screw on cap from the integrating sphere and cover the opening with the diaphragm. Place the hole over the center. If the diaphragm was created with one light absorbing and one light reflecting side, place the light absorbing side up and the light reflecting side down, facing the inside of the integrating sphere. 
		Note: To prevent dust and debris from entering the integrating sphere and to keep the hole centered, secure the diaphragm to the outside of the integrating sphere with lab tape.</li>
	</ol>
	</li>
	<li>Measure light output along the tip in 500 &#181;m increments using a micromanipulator or stereotaxic arm and an integrating sphere. 
	Note: Safety goggles of the appropriate wavelength should be worn whenever the laser is on.
	<ol>
		<li>Connect the opposite end of the fiber to a laser or light source, but do not trigger light output yet.</li>
		<li>Secure the illuminator to a stereotaxic holder (preferably with lab tape) with the tip 7 - 10 mm below the bottom of the holder.</li>
		<li>Screw the stereotaxic holder into the stereotaxic arm.</li>
		<li>Align the tip of the illuminator with the hole in the center of the diaphragm. Zero the micromanipulator when the tip is at the exact same level as the diaphragm.</li>
		<li>Turn off the room lights and zero the integrating sphere.</li>
		<li>Trigger the laser (or other light source) and measure the total light power output using the integrating sphere. 
		Note: Use the lowest light output possible for calibration testing.</li>
		<li>Lower the fiber 500 &#181;m into the integrating sphere and repeat step 2.2.6.</li>
		<li>Continue lowering the fiber into the integrating sphere and measuring total light output in 500 &#181;m increments until the total light power levels off. 
		Caution: Total light power should level off once the entire tip is in the sphere. Do not continue to lower the fiber more than 1 - 2 mm beyond the etched tip length. If the tip contacts the bottom of the integrating sphere, it may melt and/or ruin the integrating sphere.</li>
	</ol>
	</li>
	<li>Confirm an evenly etched fiber by plotting total light power output as a function of how far the fiber has been lowered into the integrating sphere to confirm linearity.</li>
</ol>
3. In Vivo Illumination
Note: Here, these methods are shown using a plastic model rather than a non-human primate.
<ol>
	<li>Implant a 25 mm diameter recording chamber was implanted over the brain area of interest prior to experimentation.</li>
	<li>Perform anatomical magnetic resonance imaging (MRI) prior to experimentation. Place a custom recording grid in the chamber and fill it with sterile surgical lubricant to allow for grid visualization and determination of the level of the dura and target brain structures.</li>
	<li>Prepare a tower micro-drive prior to each testing session.
	<ol>
		<li>Affix a 25 gauge guide tube with beveled tip to the middle and lower clamps on the drive. Two clamps are used to ensure that the guide tube remains straight. Both of these clamps can be moved manually if desired. 
		Note: The guide tube may be epoxied or soldered to the clamps.</li>
		<li>Secure the large volume illuminator in the upper clamp on the same drive. This clamp is attached to the drive motor.</li>
		<li>Thread the large-volume illuminator through the guide tube fully and confirm that the tip of the illuminator extends past the tip of the guide tube. 
		Note: The length of illuminator that extends past the tip of the guide tube equals the distance from the dura to the lower margin of the target brain region, as determined via MRI.</li>
		<li>Soak the guide tube and illuminator in antiseptic solution (e.g., chlorohexidine) to sterilize.</li>
	</ol>
	</li>
	<li>Place a custom sterilized grid inside the clean chamber and secure it at a pre-specified orientation with a screw on the side of the chamber. The grid shown here has 1 mm spacing; however, the spacing can be customized as needed. 
	Note: This should be identical to the grid and orientation used in the anatomical MRI.</li>
	<li>Secure the stereotactic micro-drive holder on the recording chamber in a pre-determined orientation.</li>
	<li>Retract the sterilized illuminator from the guide tube by pulling the illuminator up using sterile, blunt forceps. The tip of the illuminator should be 5 - 10 mm above the tip of guide tube. 
	Note: The illuminator will bow outward between the guide tube and the clamp. This will not damage the flexible illuminator.</li>
	<li>Affix the micro-drive to the holder and place the guide tube into target grid hole.</li>
	<li>Lower the micro-drive stage until the guide tube is just through the level of the dura. 
	Note: If desired, a second micro-drive with an electrode can be placed on the stage and lowered into a different grid hole. The local field potential on this electrode will show a distance-dependent light artifact, which can be used to confirm illuminator placement.</li>
	<li>Attempt the lower the illuminator manually with sterile forceps.
	<ol>
		<li>If there is any resistance, retract the illuminator 5 - 10 mm, wait 10 min to allow the tissue to settle and try again.</li>
		<li>If there is still resistance on the second attempt, retract the illuminator tip into the guide tube, lower the guide tube 0.25 mm, and try again.</li>
		<li>Repeat until the illuminator slides through the guide tube without any resistance.</li>
		<li>Lower the illuminator until it is taut. 
		Caution: Do not push the illuminator forcefully against resistance. In these cases the guide tube typically has not penetrated the dura fully. Pushing the fiber forcefully will cause it to bend on itself, preventing the fiber from entering the brain and possibly destroying the tip (Figure 1g).</li>
	</ol>
	</li>
	<li>Connect the ferrule on the other end of the illuminator to the larger optics set up or laser.</li>
	<li>Ensure that no light is visible to the non-human primate.
	<ol>
		<li>Use black-out shielding or light absorbing foil to fully encompass the recording towers.</li>
		<li>Place all optical connections in shielded envelopes made of light absorbing foil.</li>
		<li>Shield all patch cables with either light absorbing foil or black electrical tape.</li>
		<li>As an extra precaution, place a decoy light-emitting diode (LED) bank of the same light color used in the experiment behind the non-human primate and flash the LEDs continuously at 2.5 Hz. This prevents the eyes from adjusting fully to darkness. If there were inadvertent light leakage, this flashing light would help to prevent the leak from serving as a behavioral trigger.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Herculano-Houzel, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+human+brain+in+numbers:+a+linearly+scaled-up+primate+brain.">The human brain in numbers: a linearly scaled-up primate brain.</a> Front Hum Neurosci. 3, 31 (2009).</li><li>Tamura, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+glass-coated+tungsten+microelectrode+enclosing+optical+fibers+for+optogenetic+exploration+in+primate+deep+brain+structures.">A glass-coated tungsten microelectrode enclosing optical fibers for optogenetic exploration in primate deep brain structures.</a> J Neurosci Meth. 211 (1), 49-57 (2012).</li><li>Diester, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+optogenetic+toolbox+designed+for+primates.">An optogenetic toolbox designed for primates.</a> Nat Neurosci. 14 (3), 387-397 (2011).</li><li>Dai, J., Brooks, D. I., Sheinberg, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+and+Electrical+Microstimulation+Systematically+Bias+Visuospatial+Choice+in+Primates.">Optogenetic and Electrical Microstimulation Systematically Bias Visuospatial Choice in Primates.</a> Curr biol. 24 (1), 63-69 (2014).</li><li>Ozden, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+coaxial+optrode+as+multifunction+write-read+probe+for+optogenetic+studies+in+non-human+primates.">A coaxial optrode as multifunction write-read probe for optogenetic studies in non-human primates.</a> J Neurosci Meth. 219 (1), 142-154 (2013).</li><li>Ruiz, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetics+through+windows+on+the+brain+in+the+nonhuman+primate.">Optogenetics through windows on the brain in the nonhuman primate.</a> J Neurophysiol. 110 (6), 1455-1467 (2013).</li><li>Chuong, A. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Noninvasive+optical+inhibition+with+a+red-shifted+microbial+rhodopsin.">Noninvasive optical inhibition with a red-shifted microbial rhodopsin.</a> Nat Neurosci. 17 (8), 1123-1129 (2014).</li><li>Acker, L., Pino, E. N., Boyden, E. S., Desimone, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FEF+inactivation+with+improved+optogenetic+methods.">FEF inactivation with improved optogenetic methods.</a> Proc Natl Acad Sci U S A. 113 (46), 7297-7306 (2016).</li><li>Jazayeri, M., Lindbloom-Brown, Z., Horwitz, G. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Saccadic+eye+movements+evoked+by+optogenetic+activation+of+primate+V1.">Saccadic eye movements evoked by optogenetic activation of primate V1.</a> Nat Neurosci. 15 (10), 1368-1370 (2012).</li><li>Gerits, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetically+Induced+Behavioral+and+Functional+Network+Changes+in+Primates.">Optogenetically Induced Behavioral and Functional Network Changes in Primates.</a> Curr Biol. 22 (18), 1722-1726 (2012).</li><li>Ohayon, S., Grimaldi, P., Schweers, N., Tsao, D. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Saccade+modulation+by+optical+and+electrical+stimulation+in+the+macaque+frontal+eye+field.">Saccade modulation by optical and electrical stimulation in the macaque frontal eye field.</a> J Neurosci. 33 (42), 16684-16697 (2013).</li><li>Cavanaugh, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+inactivation+modifies+monkey+visuomotor+behavior.">Optogenetic inactivation modifies monkey visuomotor behavior.</a> Neuron. 76 (5), 901-907 (2012).</li></ol>

While optogenetic tools are widely used to study disease and physiology in rodents, the technical challenge of illuminating large brain volumes has limited the use of optogenetics in non-human primates. Pioneering studies in monkeys used large light power densities (~100 mW/mm2 to 20 W/mm2) to illuminate small volumes, perhaps &#60; 1 mm3, and reported modest behavioral effects with excitatory opsins in the cortex4,9,<s...

Optogenetic tools, which allow for millisecond-precise, light-driven neuronal control are widely used to study functional physiology and behavior in rodents and invertebrates. However, technical challenges have limited the use of optogenetics in the non-human primate brain, which has a volume ~100x larger than the rodent brain 1.
To facilitate optogenetics studies in non-human primates, an illuminator was designed to address two competing goals: large volume illumination and minimal penetration damage. Previous attempts to address one of these concerns have come at the expensive of the other. Bundles of fibers illuminate larger volumes but with increased diameter, and, thus, damage2,3. Tapered glass fibers reduce penetration damage, but narrowly focus light to light emitting surface areas &#60;100 &#181;m2 4,5. External brain illumination through a window in the dura circumvents the challenge of penetration damage and may allow for large volume illumination, but it can only be used for a few superficial brain areas6.
To create a large-volume, small diameter illuminator (Figure 1a), the tip of a plastic optical fiber is heat tapered and the core and cladding are etched (Figure 1b,c). Unlike other tapered fibers that focus light to a narrow point, the etching allows light to escape evenly out the sides of the tip, thus, distributing light broadly over a large area (Figure 1d,e). Because penetration damage is proportional to penetration diameter, this illuminator has no more penetration damage than a conventional fiber, yet it has &#62;100x the light emitting surface area and delivers light more broadly with 1/100th the light power density in a brain phantom (1.75% agarose) (Figure 1e). A Monte Carlo model (Figure 1f) illustrates the difference in light spread between a conventional fiber and the large volume illuminator when they have equal light power densities as their light emitting surfaces. Each illuminator is individually calibrated using an integrating sphere (Figure 2a,b) to ensure even light distribution along the tip (Figure 2c).
This large volume illuminator has been validated with optogenetic manipulation of both behavior and neuronal firing in non-human primates. The fiber tip length may be customized to any brain area and to each animal&#8217;s individual receptive field map. The illuminator may be paired with a penetrating electrode for neuronal recordings that span the length of illumination. Further, because the fiber can carry any color of visible light, it can be paired with any of the available optogenetic molecules available.

<table><tbody><tr><td>Plastic optical fiber</td><td>Industrial fiber optics</td><td>SK-10</td><td>250 micron diameter, Super Eska line</td></tr><tr><td>Wire stripper</td><td>Klein Tools</td><td>11047</td><td>22 gauge</td></tr><tr><td>Vise Clamp</td><td>Wilton</td><td>11104</td><td>Generic table mount vice clamp</td></tr><tr><td>Dual temperature heat gun</td><td>Milwaukee</td><td>8975-6</td><td>570 / 1,000 &amp;deg;F</td></tr><tr><td>Lab marker</td><td>VWR</td><td>52877</td><td></td></tr><tr><td>Dissection microscope</td><td>VistaVision</td><td>82027-156</td><td>Stereo microscope w/ dual incandescent light, 2X/4X magnification, available from VWR</td></tr><tr><td>Lab tape</td><td>VWR</td><td>89097-972</td><td>4 pack of violet color; however, tape color does not matter</td></tr><tr><td>Silicon carbide lapping sheet</td><td>ThorLabs</td><td>LF5P</td><td>5 micron grit, 10 pack</td></tr><tr><td>Aluminum oxide lapping sheet</td><td>ThorLabs</td><td>LF3P</td><td>3 micron grit, 10 pack</td></tr><tr><td>Aluminum oxide lapping&amp;nbsp; sheet</td><td>ThorLabs</td><td>LF1P</td><td>1 micron grit, 10 pack</td></tr><tr><td>Calcined alumina lapping sheet</td><td>ThorLabs</td><td>LF03P</td><td>0.3 micron grit, 10 pack</td></tr><tr><td>Hot knife</td><td>Industrial fiber optics</td><td>IF370012</td><td>60 Watt, heavy duty</td></tr><tr><td>Fiber inspection scope</td><td>ThorLabs</td><td>FS201</td><td>optional</td></tr><tr><td>Stainless Steel Ferrule</td><td>Precision fiber optics</td><td>MM-FER2003SS-265</td><td>265 micron inner diameter</td></tr><tr><td>1 mL syringe</td><td>BD</td><td>14-823-30</td><td>Luer-lok tip is preferable to reduce risk of leakage, but not strictly needed</td></tr><tr><td>Plastic epoxy</td><td>Industrial fiber optics</td><td>40 0005</td><td></td></tr><tr><td>18 gauge blunt needle</td><td>BD</td><td>305180</td><td>1.5 inch length</td></tr><tr><td>Lint-free wipe (KimWipe)</td><td>ThorLabs</td><td>KW32</td><td>available from many vendors</td></tr><tr><td>Light absorbing foil</td><td>ThorLabs</td><td>BKF12</td><td></td></tr><tr><td>Electrical tape</td><td>3M</td><td>Temflex 1700</td><td>Optional, may substitute other brands / models</td></tr><tr><td>26 gauge sharp needle&amp;nbsp;</td><td>BD</td><td>305111</td><td>0.5 inch length</td></tr><tr><td>Micromanipulator</td><td>Siskiyou</td><td>70750000E</td><td>may substitute other brands/models</td></tr><tr><td>Steretactic arm</td><td>Kopf</td><td>1460</td><td>may substitute other brands/models</td></tr><tr><td>Laser safety goggles</td><td>KenTeK</td><td>KCM-6012</td><td>must be selected based on the color of laser used, example given here</td></tr><tr><td>Laser or other light source</td><td>vortran</td><td>Stradus 473-50</td><td>example of blue laser</td></tr><tr><td>Integrating sphere</td><td>ThorLabs</td><td>S142C</td><td>Attached power meter, also available from ThorLabs, item #PM100D</td></tr><tr><td>Ultem recording chamber</td><td>Crist instrument company</td><td>6-ICO-J0</td><td>Customized with alignment notch</td></tr><tr><td>Tower microdrive with clamps</td><td>NAN</td><td>DRTBL-CMS</td><td></td></tr><tr><td>Guide tube</td><td>Custom</td><td>N/A</td><td>Made from 25 gauge spinal needle (BD) or blunt tubing</td></tr><tr><td>NAN driver system</td><td>NAN</td><td>NANDrive</td><td></td></tr><tr><td>Custom grid design</td><td>custom</td><td>custom</td><td>plans available upon request</td></tr><tr><td>Blunt forceps</td><td>FischerScientific</td><td>08-875-8A</td><td>generic stainless steel blunt forceps</td></tr><tr><td>Digital calipers</td><td>Neiko</td><td>01407A</td><td>available on amazon.com. May select a finer resolution caliper for more precise measurements.</td></tr><tr><td>Patch cable</td><td>ThorLabs</td><td>FG200LCC-custom</td><td>This is one example of many possible patch cables. As long as the fiber diameter is less than or equal to the fiber diameter of the large volume illuminator and as long as the connectors interface, any patch cable (glass or plastic, vendor purchased or made in the lab) is fine for this application.</td></tr><tr><td>Clear plastic dust caps</td><td>ThorLabs</td><td>CAPF</td><td>Package of 25</td></tr><tr><td>ceramic split mating sleeve</td><td>Precision Fiber Products, Inc.</td><td>SM-CS1140S</td><td></td></tr></tbody></table>

large volume, behaviorally-relevant illumination for optogenetics in non-human primates

This protocol describes a large-volume illuminator, which was developed for optogenetic manipulations in the non-human primate brain. The illuminator is a modified plastic optical fiber with etched tip, such that the light emitting surface area is &#62; 100x that of a conventional fiber. In addition to describing the construction of the large-volume illuminator, this protocol details the quality-control calibration used to ensure even light distribution. Further, this protocol describes techniques for inserting and removing the large volume illuminator. Both superficial and deep structures may be illuminated. This large volume illuminator does not need to be physically coupled to an electrode, and because the illuminator is made of plastic, not glass, it will simply bend in circumstances when traditional optical fibers would shatter. Because this illuminator delivers light over behaviorally-relevant tissue volumes (&#8776; 10 mm3) with no greater penetration damage than a conventional optical fiber, it facilitates behavioral studies using optogenetics in non-human primates.

The illumination of large brain volumes in non-human primates allows for behaviorally-relevant optogenetic manipulation. Acker et al. (2016) used this large volume illuminator with the red-shifted Halorhodopsin, Jaws 7 to study the temporal contribution of the frontal eye field (FEF) to memory-guided saccades in two rhesus monkeys. Specifically, FEF neurons were injected with a viral vector containing Jaws and then illuminated with red-light using the large volume illuminator during eithe...

Watch this Scientific Journal Video about Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates at JoVE.com

Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates

A protocol to build a tissue penetrating illuminator for delivering light over large volumes with minimal diameter is presented.

This protocol describes a large-volume illuminator, which was developed for optogenetic manipulations in the non-human primate brain. The illuminator is a ...

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8.0K Views.  Massachusetts Institute of Technology. Een protocol bij het bouwen van een weefsel doordringende illuminator voor het leveren van licht via grote volumes met minimale diameter wordt gepresenteerd.

Video: Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates

Selective Viral Transduction of Adult-born Olfactory Neurons for Chronic in vivo Optogenetic Stimulation

Local interneurons are continuously regenerated in the olfactory bulb of adult rodents1-3. In this process, called adult neurogenesis, neural stem cells in the walls of the lateral ventricle give rise to neuroblasts that migrate for several millimeters along the rostral migratory stream (RMS) to reach and incorporate into the olfactory bulb. To study the different steps and the impact of adult-born neuron integration into preexisting olfactory circuits, it is necessary to selectively label and manipulate the activity of this specific population of neurons. The recent development of optogenetic technologies offers the opportunity to use light to precisely activate this specific cohort of neurons without affecting surrounding neurons4,5. Here, we present a series of procedures to virally express Channelrhodopsin2(ChR2)-YFP in a temporally restricted cohort of neuroblasts in the RMS before they reach the olfactory bulb and become adult-born neurons. In addition, we show how to implant and calibrate a miniature LED for chronic in vivo stimulation of ChR2-expressing neurons.

Selective Viral Transduction of Adult-born Olfactory Neurons for Chronic in vivo Optogenetic Stimulation

Adult-born neurons of the olfactory bulb can be optogenetically controlled using Channelrhodopsin2-expressing lentiviral injection in the rostral migratory stream and chronic photostimulation with an implanted miniature LED.

Local interneurons are continuously regenerated in the olfactory bulb of adult rodents1-3. In this process, called adult neurogenesis, neural stem cells ...

Neuroscience

A Method for High Fidelity Optogenetic Control of Individual Pyramidal Neurons In vivo

Optogenetic methods have emerged as a powerful tool for elucidating neural circuit activity underlying a diverse set of behaviors across a broad range of species. Optogenetic tools of microbial origin consist of light-sensitive membrane proteins that are able to activate (e.g., channelrhodopsin-2, ChR2) or silence (e.g., halorhodopsin, NpHR) neural activity ingenetically-defined cell types over behaviorally-relevant timescales. We first demonstrate a simple approach for adeno-associated virus-mediated delivery of ChR2 and NpHR transgenes to the dorsal subiculum and prelimbic region of the prefrontal cortex in rat. Because ChR2 and NpHR are genetically targetable, we describe the use of this technology to control the electrical activity of specific populations of neurons (i.e., pyramidal neurons) embedded in heterogeneous tissue with high temporal precision. We describe herein the hardware, custom software user interface, and procedures that allow for simultaneous light delivery and electrical recording from transduced pyramidal neurons in an anesthetized in vivo preparation. These light-responsive tools provide the opportunity for identifying the causal contributions of different cell types to information processing and behavior.

A Method for High Fidelity Optogenetic Control of Individual Pyramidal Neurons In vivo

The recent development of neuroscience tools that combine genetics and optics, termed "optogenetics", enables control over neural circuit activity with an unprecedented level of spatial and temporal resolution. Here we provide a protocol for integrating in vivo recording with optogenetic manipulation of genetically-defined subsets of prefrontal cortical and subicular pyramidal neurons.

Optogenetic methods  have emerged as a powerful tool for elucidating neural circuit activity  underlying a diverse set of behaviors across a broad range ...

Optogenetic Manipulation of Neuronal Activity to Modulate Behavior in Freely Moving Mice

Optogenetic modulation of neuronal circuits in freely moving mice affects acute and long-term behavior. This method is able to perform manipulations of single neurons and region-specific transmitter release, up to whole neuronal circuitries in the central nervous system, and allows the direct measurement of behavioral outcomes. Neurons express optogenetic tools via an injection of viral vectors carrying the DNA of choice, such as Channelrhodopsin2 (ChR2). Light is brought into specific brain regions via chronic optical implants that terminate directly above the target region. After two weeks of recovery and proper tool-expression, mice can be repeatedly used for behavioral tests with optogenetic stimulation of the neurons of interest.
Optogenetic modulation has a high temporal and spatial resolution that can be accomplished with high cell specificity, compared to the commonly used methods such as chemical or electrical stimulation. The light does not harm neuronal tissue and can therefore be used for long-term experiments as well as for multiple behavioral experiments in one mouse. The possibilities of optogenetic tools are nearly unlimited and enable the activation or silencing of whole neurons, or even the manipulation of a specific receptor type by light.
The results of such behavioral experiments with integrated optogenetic stimulation directly visualizes changes in behavior caused by the manipulation. The behavior of the same animal without light stimulation as a baseline is a good control for induced changes. This allows a detailed overview of neuronal types or neurotransmitter systems involved in specific behaviors, such as anxiety. The plasticity of neuronal networks can also be investigated in great detail through long-term stimulation or behavioral observations after optical stimulation. Optogenetics will help to enlighten neuronal signaling in several kinds of neurological diseases.

With optogenetic manipulation of specific neuronal populations or brain regions, behavior can be modified with high temporal and spatial resolution in freely moving animals. By using different optogenetic tools in combination with chronically implanted optical fibers, a variety of neuronal modulations and behavioral testing can be performed.

Optogenetic modulation of neuronal circuits in freely moving mice affects acute and long-term behavior. This method is able to perform manipulations of ...

Bioluminescent Optogenetics 2.0: Harnessing Bioluminescence to Activate Photosensory Proteins In Vitro and In Vivo

Bioluminescence - light emitted by a luciferase enzyme oxidizing a small molecule substrate, a luciferin - has been used in vitro and in vivo to activate light-gated ion channels and pumps in neurons. While this bioluminescent optogenetics (BL-OG) approach confers a chemogenetic component to optogenetic tools, it is not limited to use in neuroscience. Rather, bioluminescence can be harnessed to activate any photosensory protein, thus enabling the manipulation of a multitude of light-mediated functions in cells. A variety of luciferase-luciferin pairs can be matched with photosensory proteins requiring different wavelengths of light and light intensities.
Depending on the specific application, efficient light delivery can be achieved by using luciferase-photoreceptor fusion proteins or by simple co-transfection. Photosensory proteins based on light-dependent dimerization or conformational changes can be driven by bioluminescence to effect cellular processes from protein localization, regulation of intracellular signaling pathways to transcription. The protocol below details the experimental execution of bioluminescence activation in cells and organisms and describes the results using bioluminescence-driven recombinases and transcription factors. The protocol provides investigators with the basic procedures for carrying out bioluminescent optogenetics in vitro and in vivo. The described approaches can be further extended and individualized to a multitude of different experimental paradigms.

Bioluminescent Optogenetics 2.0: Harnessing Bioluminescence to Activate Photosensory Proteins In Vitro and In Vivo

Bioluminescence-light emitted by a luciferase enzyme oxidizing a small-molecule substrate, a luciferin-can be harnessed to activate photosensory proteins, thereby adding another dimension to light stimulation and enabling the manipulation of a multitude of light-mediated functions in cells across temporal and spatial scales.

Bioluminescence - light emitted by a luciferase enzyme oxidizing a small molecule substrate, a luciferin - has been used in vitro and in vivo to activate ...

Biochemistry

In vivo Optogenetic Stimulation of the Rodent Central Nervous System

The ability to probe defined neural circuits in awake, freely-moving animals with cell-type specificity, spatial precision, and high temporal resolution has been a long sought tool for neuroscientists in the systems-level search for the neural circuitry governing complex behavioral states. Optogenetics is a cutting-edge tool that is revolutionizing the field of neuroscience and represents one of the first systematic approaches to enable causal testing regarding the relation between neural signaling events and behavior. By combining optical and genetic approaches, neural signaling can be bi-directionally controlled through expression of light-sensitive ion channels (opsins) in mammalian cells. The current protocol describes delivery of specific wavelengths of light to opsin-expressing cells in deep brain structures of awake, freely-moving rodents for neural circuit modulation. Theoretical principles of light transmission as an experimental consideration are discussed in the context of performing in vivo optogenetic stimulation. The protocol details the design and construction of both simple and complex laser configurations and describes tethering strategies to permit simultaneous stimulation of multiple animals for high-throughput behavioral testing.

In vivo Optogenetic Stimulation of the Rodent Central Nervous System

Optogenetics has become a powerful tool for use in behavioral neuroscience experiments. This protocol offers a step-by-step guide to the design and set-up of laser systems, and provides a full protocol for carrying out multiple and simultaneous in vivo optogenetic stimulations compatible with most rodent behavioral testing paradigms.

The ability to probe defined neural circuits in awake, freely-moving animals with cell-type specificity, spatial precision, and high temporal resolution ...

A Guide to In vivo Single-unit Recording from Optogenetically Identified Cortical Inhibitory Interneurons

A major challenge in neurophysiology has been to characterize the response properties and function of the numerous inhibitory cell types in the cerebral cortex. We here share our strategy for obtaining stable, well-isolated single-unit recordings from identified inhibitory interneurons in the anesthetized mouse cortex using a method developed by Lima and colleagues1. Recordings are performed in mice expressing Channelrhodopsin-2 (ChR2) in specific neuronal subpopulations. Members of the population are identified by their response to a brief flash of blue light. This technique &#8211; termed &#8220;PINP&#8221;, or Photostimulation-assisted Identification of Neuronal Populations &#8211; can be implemented with standard extracellular recording equipment. It can serve as an inexpensive and accessible alternative to calcium imaging or visually-guided patching, for the purpose of targeting extracellular recordings to genetically-identified cells. Here we provide a set of guidelines for optimizing the method in everyday practice. We refined our strategy specifically for targeting parvalbumin-positive (PV+) cells, but have found that it works for other interneuron types as well, such as somatostatin-expressing (SOM+) and calretinin-expressing (CR+) interneurons.

A Guide to In vivo Single-unit Recording from Optogenetically Identified Cortical Inhibitory Interneurons

Here we describe our strategy for obtaining stable, well-isolated single-unit recordings from identified inhibitory interneurons in the anesthetized mouse cortex. Neurons expressing ChR2 are identified by their response to blue light. The method uses standard extracellular recording equipment, and serves as an inexpensive alternative to calcium imaging or visually-guided patching.

A major challenge in neurophysiology has been to characterize the response properties and function of the numerous inhibitory cell types in the cerebral ...

Optogenetic Functional MRI

The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional magnetic resonance imaging (ofMRI), which is a novel technique that combines the relatively high spatial resolution of high-field fMRI with the precision of optogenetic stimulation. Fiber optics that enable delivery of specific wavelengths of light deep into the brain in vivo are implanted into regions of interest in order to specifically stimulate targeted cell types that have been genetically induced to express light-sensitive trans-membrane conductance channels, called opsins. fMRI is used to provide a non-invasive method of determining the brain's global dynamic response to optogenetic stimulation of specific neural circuits through measurement of the blood-oxygen-level-dependent (BOLD) signal, which provides an indirect measurement of neuronal activity. This protocol describes the construction of fiber optic implants, the implantation surgeries, the imaging with photostimulation and the data analysis required to successfully perform ofMRI. In summary, the precise stimulation and whole-brain monitoring ability of ofMRI are crucial factors in making ofMRI a powerful tool for the study of the connectomics of the brain in both healthy and diseased states.

This protocol describes the steps and data analysis required to successfully perform optogenetic functional magnetic resonance imaging (ofMRI). ofMRI is a novel technique that combines high-field fMRI readout with optogenetic stimulation, allowing for cell type-specific mapping of functional neural circuits and their dynamics across the whole living brain.

The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional ...

A MRI-Based Toolbox for Neurosurgical Planning in Nonhuman Primates

In this paper, we outline a method for surgical preparation that allows for the practical planning of a variety of neurosurgeries in NHPs solely using data extracted from magnetic resonance imaging (MRI). This protocol allows for the generation of 3D printed anatomically accurate physical models of the brain and skull, as well as an agarose gel model of the brain modeling some of the mechanical properties of the brain. These models can be extracted from MRI using brain extraction software for the model of the brain, and custom code for the model of the skull. The preparation protocol takes advantage of state-of-the-art 3D printing technology to make interfacing brains, skulls, and molds for gel brain models. The skull and brain models can be used to visualize brain tissue inside the skull with the addition of a craniotomy in the custom code, allowing for better preparation for surgeries directly involving the brain. The applications of these methods are designed for surgeries involved in neurological stimulation and recording as well as injection, but the versatility of the system allows for future expansion of the protocol, extraction techniques, and models to a wider scope of surgeries.

The method outlined below aims to provide a comprehensive protocol for the preparation of nonhuman primate (NHP) neurosurgery using a novel combination of three-dimensional (3D) printing methods and MRI data extraction.

In this paper, we outline a method for surgical preparation that allows for the practical planning of a variety of neurosurgeries in NHPs solely using ...

Bioengineering

Convection Enhanced Delivery of Optogenetic Adeno-associated Viral Vector to the Cortex of Rhesus Macaque Under Guidance of Online MRI Images

In non-human primate (NHP) optogenetics, infecting large cortical areas with viral vectors is often a difficult and time-consuming task. Here, we demonstrate the use of magnetic resonance (MR)-guided convection enhanced delivery (CED) of optogenetic viral vectors into primary somatosensory (S1) and motor (M1) cortices of macaques to obtain efficient, widespread cortical expression of light-sensitive ion channels. Adeno-associated viral (AAV) vectors encoding the red-shifted opsin C1V1 fused to yellow fluorescent protein (EYFP) were injected into the cortex of rhesus macaques under MR-guided CED. Three months post-infusion, epifluorescent imaging confirmed large regions of optogenetic expression (&#62;130 mm2) in M1 and S1 in two macaques. Furthermore, we were able to record reliable light-evoked electrophysiology responses from the expressing areas using micro-electrocorticographic arrays. Later histological analysis and immunostaining against the reporter revealed widespread and dense optogenetic expression in M1 and S1 corresponding to the distribution indicated by epifluorescent imaging. This technique enables us to obtain expression across large areas of the cortex within a shorter period of time with minimal damage compared to the traditional techniques and can be an optimal approach for optogenetic viral delivery in large animals such as NHPs. This approach demonstrates great potential for network-level manipulation of neural circuits with cell-type specificity in animal models evolutionarily close to humans.&#160;

Here, we demonstrate magnetic resonance (MR)-guided convection enhanced delivery (CED) of viral vectors into the cortex as an efficient and simplified approach for achieving optogenetic expression across large cortical areas in the macaque brain.

In non-human primate (NHP) optogenetics, infecting large cortical areas with viral vectors is often a difficult and time-consuming task. Here, we ...

Automated 3D Brain and Skull Modeling from MRI for NHP Neurosurgical Planning

A Neural Implant Design Toolbox for Nonhuman Primates

This paper describes an in-house method of 3D brain and skull modeling from magnetic resonance imaging (MRI) tailored for nonhuman primate (NHP) neurosurgical planning. This automated, computational software-based technique provides an efficient way of extracting brain and skull features from MRI files as opposed to traditional manual extraction techniques using imaging software. Furthermore, the procedure provides a method for visualizing the brain and craniotomized skull together for intuitive, virtual surgical planning. This generates a drastic reduction in time and resources from those required by past work, which relied on iterative 3D printing. The skull modeling process creates a footprint that is exported into modeling software to design custom-fit cranial chambers and headposts for surgical implantation. Custom-fit surgical implants minimize gaps between the implant and the skull that could introduce complications, including infection or decreased stability. By implementing these pre-surgical steps, surgical and experimental complications are reduced. These techniques can be adapted for other surgical processes, facilitating more efficient and effective experimental planning for researchers and, potentially, neurosurgeons.

Author Spotlight: Streamlined Brain and Skull Modeling for Enhanced Neurosurgical Planning in NHP Research

This paper outlines automated processes for nonhuman primate neurosurgical planning based on magnetic resonance imaging (MRI) scans. These techniques use procedural steps in programming and design platforms to support customized implant design for NHPs. The validity of each component can then be confirmed using three-dimensional (3D) printed life-size anatomical models.

Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates

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