Table of Contents

Table of Contents-------------------------------------------------------------------------------- 2
Description of Benchmark Stereotaxic Instrument------------------------------------------ 3
Manipulator Movements and Offsets --------------------------------------------------------- 4
Alignment and Calibration --------------------------------------------------------------------- 5
Installing Animal and Operating -------------------------------------------------------------- 6
Care and Cleaning ------------------------------------------------------------------------------- 9
Specifications ------------------------------------------------------------------------------------ 10
Useful References ------------------------------------------------------------------------------- 11
Warranty------------------------------------------------------------------------------------------ 11
Appendix A Vernier Scales ------------------------------------------------------------------- 12
Appendix B Initial Assembly of Digital ----------------------------------------------------- 13

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Description of Benchmark Stereotaxic Instruments
A stereotaxic instrument is a device for placing a probe in a precise anatomical location in the brain or
spinal cord of an animal. It consists of two major sections that must be in alignment with each other,
1) a head or spinal holder for an animal that locks the target in a defined position and orientation, and 2)
a manipulator to enable precise movements of a probe relative to the head or body.
Manipulator Movements and Offsets
Benchmark Stereotaxic Instrument manipulators all have 3 linear movements and 3 rotary movements,
as well as 2 settable offsets. These are labeled in Figure 1.
The linear movements are referred to relative to the animal:
• (A/P) Anterior/posterior, movements along a line parallel to the midline of the brain
• (M/L) Medial/Lateral, movements along a horizontal line perpendicular to the midline
• (D/V) Dorsal/Ventral, generally vertical, the last movement to advance into brain
The rotary movements are referred to by the effect on manipulator orientation:
• Rotation, changes the direction of the tilt
• Tilt, tilts the manipulator and angle of probe approach in either the A/P or M/L direction
• Swing-Out, swivels the probe out of the way, and then restores it precisely to its original
position
The V clamp probe offset adaptor shifts the range of a movement to reach a different area
• The probe offset adaptor set screw can be loosened to vertically move the probe in the D/V
direction, and then relocked
• The probe holder offset clamp can be flipped to offset in the anterior or posterior direction, and
has two holes for the thumb screw giving the user two choices for the degree of offset, four
possible positions, two rostral, and two caudal, to the manipulator
Other optional offsets are available for special needs. If you have a special request, please contact us.

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 Figure 1. Movements and Offsets of Stereotaxic Instrument

Swing Out is a tapered square block that allows the M/L drive to point in any of 4 directions. It is used
to move the probe holder away from the skull, e.g. in order to drill a hole, and then return to exactly the
position it was in, defined by the block face. Using the Rotation to achieve this purpose will give
substantially less accuracy of return. To operate, push up and around after loosening locking screw.

Tilt is a pivot movement that allows tilting the probe holder to approach brain at an angle. In Figure 1,
tilt is oriented to allow tilt in the A/P plane. It may be made to tilt in the M/L plane by turning the
Rotation movement 90˚ either way, then turn the Swing Out 90˚ back to its M/L orientation. Tilt
would then be possible in the M/L plane. Obviously, complex angles of tilt can be achieved by
manipulating the rotation less than 90˚. This capability is rarely used with stereotaxic instruments less
sophisticated than the Benchmark Angle One™ or Angle Two™, as it then becomes very difficult to
calculate where the movements will take the probe tip.

Rotation has no stops or tapered faces, so is free to rotate any number of degrees. The distance from the
pivot point to the graduations for this movement is much less than the distance from the pivot to the
probe holder. Therefore, very small errors of graduated mark alignment produce multifold larger errors
of probe tip position. Any time the Rotation is used, alignment should be rechecked. (See the procedure
in Alignment and Calibration.)

The clamp that attaches the shaft of the probe holder to the manipulator includes two offset mechanisms.
Vertical Offset is achieved by loosening the set screw with a 5/64 inch Allen hex wrench, sliding the
shaft up or down, and retightening the set screw. At this time, the shaft can also be rotated.
A/P Offset is achieved in two ways. The user may select from two holes through the clamp that will
accommodate the thumb screw to set the degree of offset. The user may also remove the clamp from the

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probe holder, and flip it 180˚ to change the direction of A/P offset. All probe holders available from
MyNeuroLab use the same size shaft, and the same offset clamp. The clamp comes with each probe
holder (in most cases), and can be offset as described.

The three linear movements are obvious in function. All three axis should be perpendicular to each
other, unless deliberately set at other angles (See Alignment and Calibration). For instruction on reading
Vernier scales, refer to Appendix A. If the stereotaxic instrument includes digital scales, these may be
zeroed by touching the zero buttons when the probe is at Bregma (or earbar zero if an instrument
reference is to be used as zero.)

Alignment and Calibration

Accuracy of measurement depends on the assumption that all 3 axes are perpendicular to each other (or,
if tilt or rotation is used, at a known angle relative to each other.) The Rotation movement in particular
can easily be slightly out of alignment and impair accuracy. For the Benchmark Basic, Digital and
Deluxe, good alignment may be achieved by a visual gap method (below). Please note that the Angle
One™ and Angle Two™ include an alignment tool kit and corresponding manual. This kit may be
purchased separately for use with other stereotaxic instruments. With any stereotaxic instrument, check
alignment and probe straightness before starting any projects and after probe changes.

The human eye can see very small differences, tens of microns, in the size of an air gap between two
objects. This can be used to check alignment of the manipulator axes with the head holder, and the
straightness of the probe before use.

To check alignment, install a probe, either known straight (a drill bit or glass pipette blank), or the actual
probe to be used. The standard probe holder has 10 grooves in the plastic block on each of 3 faces that
run parallel to the probe holder shaft (the fourth such face is flat and ungrooved. Lay the probe in one of
the grooves, and tighten the clamp to secure it in place.

Push both earbars in to where they touch in the middle. Both earbars vernier zero should align with zero
on the scales. Tighten the locking levers. If they do not read zero, the scales were misaligned at the
factory. The scales can be adjusted, but should be adjusted when the earbars meet in the center between
the U frame arms. If you do not have the equipment to measure this, you might want to send the
instrument to the factory for alignment.

Use the 3 linear movement drives to move the probe until it is next to an earbar, just separated from it by
a barely visible air gap. Move the M/L drive from one side to the other, while closely watching the air
gap. If the gap gets larger or smaller, the probe is not moving parallel to the earbars, and Rotation is out
of alignment. Loosen the locking screw on the Rotation mechanism (Figure 1) and rotate slightly to
restore alignment. Relock. Try again. By trial and error, you will achieve alignment.

Unlock and rotate an ear bar 180°, so the blunt end is on the inside of the stereotaxic U frame. Relock.
Move the probe until it is a barely visible air gap away from the blunt end. Operate the D/V drive while
observing the air gap. If the air gap changes in size as the probe moves vertically, the probe is not
straight in an M/L plane. The probe may be bent or not installed straight in a groove of the probe
holder, or the tilt mechanism may be slightly tilted. Adjust the tilt, or straighten the probe. Repeat with
the probe a barely visible air gap away from one side of the ear bar. If the air gap changes in size, the

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probe is not properly aligned in an A/P plane.

Position the probe just above an earbar, with a small air gap down to the earbar. Move horizontally
along the earbar, and back and forth in the anterior/posterior direction across the earbar. If the air gap to
the tip changes in size, the instrument is moving in the vertical dimension when the other drives are
being operated.

If you have performed all three linear movement tests, and cannot align your instrument, call
MyNeuroLab for assistance.

Both the vernier and digital scales are permanently engraved by a laser guided by a computer. Just as
the lines on a ruler can not move once made, the instrument can not become un-calibrated in this sense.

Installing the Animal and Operating.

The animal’s head must be securely and symmetrically affixed in the stereotaxic instrument,
reproducibly aligned with the movement axes of the manipulator section. Different head holder
adaptors are designed for each species. For most species, bars into the ear canal on each side and a bar
behind the incisors provide a stable, reproducible and defined hold. Traditional 18˚ ear bar tapers break
the tympanic membrane. Tapers of 45˚ are almost as stable, and do not break the tympanic membrane,
and are thus better if post-surgical testing is planned. An excellent book, photographically revealing
each detailed step for stereotaxic surgery in the rat, is available from MyNeuroLab. MyNeuroLab
recommends, “Stereotaxic Surgery in the Rat, a Photographic Series” By R. J. Cooley and C.H.
Vanderwolf., even it you intend to work with a different species.

Installing the earbars is the most difficult skill required for stereotaxic surgery. If a novice, practice
with an injection anesthetized animal or a sacrificed animal. Learn to feel the correct placement before
beginning on an experimental animal. Note that the earbar locks on the Benchmark are unique locking
levers. Other companies use thumb screws, which require at least two fingers. You will notice the ease
of one-finger locking of the last earbar when installing an animal.

Anesthetize the animal and shave its head. If using gas anesthesia, go back to the induction chamber
and re-anesthetize. Install the earbars. Set the left earbar tip about 1 cm left of the center position, and
lock it in place. Remove the right earbar, and leave the lock ready to drop the earbar back into place.
Loosen the thumb screw that holds the incisor bar in place, and slide the incisor bar plate all the way
back away from the animal.

Holding the animal’s body with the left hand, and its head with the right hand, move the animal to insert
the left earbar fully into the ear canal. Pointing the nose slightly to the right, allowing the earbar to enter
from a slightly dorsal-caudal direction, will ease insertion. When the earbar slips into the canal, hold the
head in place with the left hand, and pick up the right earbar. Moving the right earbar freely, insert it
into the right ear. While holding the earbar snug in the ear, lower the body of the earbar into the right
slot and lock. Check centering. If both earbars do not have identical readings, loosen both earbar locks
while holding the bars snug from the outside with one finger, and push back and forth until both earbar
scales line up on the same number. Lock the earbars. Pushing down with one finger on either earbar
lever will lock it.

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More pressure can be applied with rat bars than with mouse bars. The mouse skull is extremely thin and
flexible, and the breathing passages run directly between the ears. The mouse is easily strangled by ear
bars. The rat earbars will not fit into mouse ear canals, and the rat tooth bar is too rounded for the
mouse. For stereotaxic mouse surgery, an optional adapter is needed, specific to the mouse. Hamsters
and gerbils fit into the rat head holder equipment.

Check that the earbars were correctly installed. Gently try to move the nose from side to side. If you
can, the earbars are not correctly placed in the ear canals or they are not snug enough. Push the nose up
and then down. If it stays right where you left it, the earbars are correctly placed. If it springs back a
bit, the earbars are probably not correctly placed. If there is movement, remove the earbars and repeat
the last paragraph.

Once the earbars are securely installed, slide the incisor bar into the mouth, hook the incisor teeth over
the bar and push the nose down. Slide the bar back until it is snug behind the incisors and lock down the
thumb screw. If using an injectable anesthetic, snugly tighten the nose clamp down. If using a gas
anesthetic, slide the nose cone forward around the animal’s nose, and unclamp the gas flow through it.

Next, place two fingers on the animals scalp, straddling the midline, where you want the incision to
begin. Pull the skin tight by pressing caudally. Set the blade of the scalpel down with some pressure
between the two fingers, sharp side down and rostral. Holding the scalpel steady, pull the skin rostrally
to cut. For a better incision, move the skin against the blade rather then the blade against the skin.
Retract the skin with locking forceps.

Scrape the scalp membranes away from the midline with the handle of the scalpel or another metal
scraping edge, in order to fully expose the bone. The midline, bregma and lambda should be visible on
the skull (Figure 3). Swab off any blood with a cotton swab, wetted with saline if needed.

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 Figure 3. Exposed Scalp with drilled holes.

The atlas you are using, particularly if by Paxinos, will describe how to locate Bregma and lambda.
The anterior point where a M/L bone suture crosses the midline suture is called Bregma. The caudal
point barely visible at the bottom of the picture, is called lambda. As you can see, the irregularity of the
biological lines makes these points somewhat indeterminate. Most atlases recommend using the best
approximation of where the intersection would be if the lines were straight and smooth, and crossed the
midline at a point. This also creates some examiner variability. You can only be consistent in how you
do it, and adjust your coordinates if need be. Use a permanent ink fine point marker to put a dot on the
bone where you think Bregma and lambda ought to be.

Use Bregma rather than the intra-aural line for the zero point (Paxinos, Watson, Pennisi, & Topple,
1985). Touch a probe down at Bregma and lambda, and take a vertical reading on the D/V at each point.
By trial and error, adjust the vertical position of the incisor bar until Bregma and lambda get the same
vertical reading. This is the ‘Skull Flat’ reference plane.

Position the probe tip at Bregma. If using a vernier model stereotaxic instrument, record the
coordinates. If using a digital stereotaxic instrument, zero the scales. Raise the probe slightly along the
D/V axis, and then move to the target A/P and M/L coordinates. Place a dot on the skull directly below

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the tip, labeling the area for drilling. Make a contralateral mark if needed. Unlock the Swing Out lock,
and pivot the manipulator and probe out of the way. Be careful the probe does not strike anything on the
way around. If need be, raise the manipulator further in the D/V direction.

The dental drill bits used for drilling into skull have a spherical head. This means that the hole is deeper
in the middle than around the edges. If you do not go deep enough, there will be bone ledges around the
outside of the hole, hidden under blood, that could break a glass pipette tip. If you go too deep in order
to remove the ledges, there may be a small lesion in cortex just under the center of the drilled hole.
Care should be taken to avoid either outcome. The smallest possible drill head, moved continuously in a
small circle as you are drilling, will help avoid either outcome. Use of a manual drill with settable depth
stops, mounted on the stereotaxic manipulator, will give you precise stereotaxic control of placement
and depth of hole, highly reproducible.

The rest is highly variable, depending on the research project. A wide variety of species adaptors and
probe holders are available for special applications.

When the surgery is complete, close with Autoclips or Tissumend suture adhesive or suture thread. Be
careful to abut cut skin to cut skin for faster healing. The small holes through the skull are insignificant
and can be ignored.

Care and Cleaning

Do not Autoclave! The bushings on the linear movements, and the acrylic block on the probe holder,
will not survive repeated autoclaving.

Do not lubricate the sliding shafts that go into plastic bushings, or the lead screw, that goes into a
plastic nut. Petroleum products will absorb on the plastic, and cause it to swell. This may result in the
opposite of the desired effect, the drive may lock up when the plastic swells after greasing or oiling.

The dovetail slides and other metal to metal sliding surfaces have a thin layer of grease lubricant. Do
not remove it with heat or solvents. Contact us for a supply of this lubricant.

Earbars and incisor bar may be sterilized with alcohol or Cidex (a commercial brand of highly dilute
glutaraldehyde). Probe holder can be sterilized with Cidex.

Wipe blood off the base plate or stainless steel parts with soapy water or alcohol.

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Specifications for Benchmark Digital Deluxe™ Stereotaxic Instrument

Resolution, all scales:

Vernier 0.1 mm
Digital Displayed 0.01 mm
Linear Advance/Revolution (screw pitch) 5 mm/rev.
Fine Drive Advance 20:1 reduction, or 0.25 mm/rev.

Manipulator Movement Ranges

AP 80 mm
ML 80 mm
DV 62.5 mm

Tilt and Rotation

ML or AP axes, or combined: ±90°
Rotation 360°

Toothbar Movement Ranges

DV 20 mm
AP 44.5 mm

Compatibility:
Earbars and nose holders interchangeable with other common makes of stereotaxic instruments.

Probe Holder:
Shaft Diameter: 7.88 mm (0.31 inches)
Length: 168 mm
Length, Extended Shaft 200 mm
Probe Holder Block 11 mm square,
10 grooves spaced at 1 mm on 3 sides
Standard Clamp Holds 0.2 to 2 mm shaft
Side Clamp Holds 0.2 to 4.5 mm shaft
“C” Clamp Holds 0.2 to 4.5 mm shaft.
Set Screw on Shaft holder: 3/32”

Second manipulator may be added on right (facing open end of “U”) side.
Power:
Digital Display – 1.5 Volt
Digital Linear Sensors – 5 Volts DC power supply (integrated circuit)

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Useful References
Paxinos G, Watson C, Pennisi M, Topple A., Bregma, lambda and the interaural midpoint in stereotaxic
surgery with rats of different sex, strain and weight. Journal of Neuroscience Methods 1: 39-43,
1985

Paxinos, G. and Watson, C. The Rat Brain in Stereotaxic Coordinates, Fourth Edition. Academic
Press, New York, 1998

Cooley, R. J, & C. H. Vanderwolf, Stereotaxic Surgery in the Rat, a Photographic Series. A.J
Kirby, 1990
 
 
 
MyNeuroLab Limited Warranty  

MyNeuroLab warrants this instrument to be free from defects in material and workmanship for a period
of one year from the date of original purchase. This warranty covers parts and labor. We may repair or
replace defective instruments at our option.
There is no warranty on consumables supplied with the instrument. The warranty does not cover
damage from abuse, neglect or use for purposes other than those intended and described in the manual.
MYNEUROLAB/CORETECH HOLDINGS DISCLAIMS ALL RESPONSIBILITY FOR
CONSEQUENTIAL DAMAGES OR INCIDENTAL LOSSES CAUSED BY USE OF THIS
INSTRUMENT, except where such disclaimer is not allowed by law. To claim, visit our website at
URL http://www.myneurolab.com and find the latest contact information, or call 314 522 0300. Do not
ship the instrument back without first contacting the company and obtaining a routing number.
This warranty gives you specific legal rights, which may vary from state to state or province to province.

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Appendix A: How to read a Vernier Scale

Your Benchmark Stereotaxic, whether digital or not, still includes the traditional Vernier scales to
measure the movement. Of course, these are redundant and little used on the digital units.

The Vernier scale allows more precise measurements that could otherwise be done with a simple ruler.
The idea was invented by Pierre Vernier A(1580-1637). A Vernier measurement requires two facing
scales. One is the main scale of any length, and graduated in standard units like a ruler. The other,
called the vernier, is short, graduated from one to ten, and graduated in units 9/10ths of the standard unit.

Figure 2. Main Scale and facing Vernier reading 1.23.

Because of this, one and only one of the lines on the vernier scale can be aligned with a graduation on
the main scale. This gives the last decimal place in the final reading. In this case it is the 3 on the
vernier. Note that the zero mark on the vernier is just after 1.2 on the main scale. And the 3 on the
vernier lines up with a mark on the main scale. The reading is 1.23.

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Appendix B: Initial assembly of Digital Instrument

Your Benchmark Digital Stereotaxic Instrument (Angle One and Two have different instructions) comes
with a single or dual display panel, appropriate to either a single or dual stereotaxic instrument. This
display panel has a power inlet near the switch, for which a power cord with a transformer in the middle
and a plug for the instrument are provided.

On the opposite side, there are 3 labeled inputs for linear encoders, using plastic telephone-like
connectors. Each is labeled, and for each there is a labeled plug connector coming from the Stereotaxic
instrument. Connect these as shown. Incorrect placement will not hurt the instrument; just that, for
example, the A/P number may change when you operate the D/V scale if you have switched those plugs.

Once everything is connected, power is connected, and the switch is on, the displays will light up and
show a number. Moving any of the stereotaxic movements will change the digital display, showing
mm’s from the zero point to 0.01 (10 microns). At any position, you may press the zeroing button, and
restore the display to zero. There is a second button on the counter, it is not assigned, has no function.

In use, with an animal installed in the stereotaxic instrument, position the probe at the zero point
(usually Bregma) and press the zero button to zero each scale. Some researchers zero the D/V scale last
when the probe touches the surface of brain. Once zero’ed, move each axis until the desired target
coordinate is displayed, and operate the DV to move down into brain.

You never need write down the zero point, do any arithmetic, or read a vernier scale.

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