Abstract:
A system and method can establish the stereotactic coordinates of anatomical targets in non-human subjects utilizing tomographic, volumetric, or projection imaging as for the purpose of doing anatomical and/or biological research. An imaging machine can produce data representative of anatomy or function in the body of the non-human subject. A mechanical reference frame can be fixed to the body of the non-human subject, and can have an associated stereotactic coordinate system. An index structure attachable or integrated with the mechanical reference frame can provide stereotactic index data in image data from the imaging machine. The stereotactic index data and the image data of the anatomy of the non-human subject can be used to develop the stereotactic coordinate positions of anatomical targets detected in the image data relative to the stereotactic coordinate system. Probe paths can be developed from desired directions to the stereotactic coordinate positions, and probe supports can guide probes along the probe paths. Various embodiments, computational techniques, and phantom bases can achieve desired research objectives.

Description:
PRIORITY CLAIM  
       [0001]     This application claims priority under 35 U.S.C. § 119(e) to U.S. Application No. 60/472,738, filed May 23, 2003, which is incorporated by reference in its entirety. 
     
    
     TECHNICAL FIELD  
       [0002]     This invention relates generally to advances in scientific systems and procedures for understanding the function and relative anatomy of non-human animals. More particularly, this invention relations to an improved method and system for the quantitative determination of positions targets, and the stereotactic positioning of probes at targets in the non-human animal anatomy, including the brain, based on MRI, CT, PET, and other imaging modalities.  
       BACKGROUND  
       [0003]     The field of human brain stereotaxy is advanced. Some stereotactic frames have been designed for use on non-human animals. Non-human stereotactic frames generally feature to brain target determination from landmarks or other markers on the skull.  
       SUMMARY  
       [0004]     In general, a bone-fixed, stereotactic, mechanical reference frame can be attached to non-human animal bony structures. A graphic reference structure attached to the mechanical reference frame can provide images of indicia located on the graphic reference structure and images of the non-human animal anatomy from MRI, CT, PET or other image scanners. Coordinates with respect to the stereotactic mechanical reference frame, of targets seen in the MRI, CT, PET or other types of images, can be determined using the images of the image indicia. Approaches to anatomical targets can be determined relative to the mechanical reference frame with probes. It is possible to determine coordinates with respect to the mechanical reference frame, of targets seen in the MRI, CT, PET or other types of image data, using the images of the image indicia. One can calculate target coordinates determined with respect to the mechanical reference frame using other image data and/or using other data sources, such as those which measure functional, neural-activity-related, atomic, or flow properties of anatomy, or those which use contrast-enhancing agents. In other examples, determination of target positions, using the graphic reference structure, that are derived from various or multiple imaging modalities, such as CT, x-ray, MRI, FMRI, DTI, MEC, EEG, phMRI, flow-sensitized MRI, and MRI with fiber-tract-tracing contrast agents, such as manganese, applied to an imaged animal subject can be achieved. In examples, the placement of probes and other instruments by a stereotactic guidance system attached to the stereotactic mechanical reference frame can be performed so that the probes are directed at calculated targets derived from the graphic reference structure. A probe can take many forms including, but not limited to, an electrode, a stimulation electrode, an ablative electrode, a recording electrode, an electrical measurement device, an electrical waveform generator, a bio-activity-monitoring device, a chemical-monitoring device, a chemical delivery device, a contrast-agent delivery device, a delivery device for neurochemical and/or genetic agents, a device for neurochemical and/or genetic monitoring, a needle, a needle configured for injection, a needle-like device, a device to be chronically implanted, and a beam of radiation.  
         [0005]     In one aspect, a method of stereotactic target localization in the body of a non-human subject includes attaching a mechanical reference frame to the bony structures of the non-human subject, the mechanical reference frame being adapted to support at least one index element and to provide index data when the mechanical reference frame with the at least one index element imaged by an imaging machine to relate the position of the mechanical reference frame to image data from the imaging machine, imaging the body of the non-human subject and the mechanical reference frame with at least one index element, by the imaging machine to provide image data of anatomical positions in the body and to provide index data from the at least one index element, to provide stereotactic data that relates the positional relationship of the mechanical reference frame and the anatomical positions, and calculating the positional relationship of a target location in the anatomical positions relative to the mechanical reference frame using the index data and the image data.  
         [0006]     The mechanical reference frame can be a head frame that is configured to be secured to the skull of a non-human animal by at least one attachment anchor. Attaching can include anchoring the at least one attachment anchor to the skull of the non-human animal. The method can include calculating a path to the target locations in relation to the mechanical reference frame based on the stereotactic data, or calculating the stereotactic coordinates associated with the image data in the stereotactic coordinate system, Calculating the path can include determining a path relative to the probe support so that a probe attached to the probe support can pass to a desired target location determined in the stereotactic data. The mechanical reference frame can include a probe support or an associated stereotactic coordinate system.  
         [0007]     In another aspect, a stereotactic system for determining the coordinate position of an anatomical target in the body of non-human subject includes a mechanical reference frame configured to be rigidly attached to the bony anatomy of the non-human subject and to have an associated three-dimensional stereotactic coordinate system, and an index structure configured to attach to the mechanical reference frame having at least one index element that produces index data in image data when the index element is imaged by an imaging machine, so that when the imaging machine images the non-human subject with the mechanical reference frame and the index structure attached, the coordinate position of the anatomical target in the non-human subject can be determined in the stereotactic coordinate system from the target image data of the anatomical target in the image data.  
         [0008]     The mechanical reference frame can include a head ring structure that is adapted to be rigidly attached to the skull of the non-human subject. The index element can include a tomographic index object that is detectable in at least one scan slice of the index structure by a tomographic imaging scanner to produce the index data. The tomographic index object can include a slice marker element which produces location data in the index data within a single tomographic image slice that define the three-dimensional coordinates of at least three non-collinear points in the stereotactic coordinate system when the index structure is attached to the mechanical reference frame. In examples, the tomographic index object can include an MRI index object that indexes data from imaging by an MRI image scanner. The slice marker element can include a diagonal element that is configured to be oriented non-parallel to the plane of the at least one image slice to produce the location data which can be used to determine the orientation of the plane of the tomographic image slice relative to the index structure. The diagonal element can include an MRI visible diagonal element that is detectable in the image data from an MRI scanner image. The system can include a probe support configured to attach to the mechanical reference frame and support a probe that is aimed at the coordinate position or a phantom base that enables developing a phantom target position on the phantom base at the coordinate position of the anatomical target, whereby the probe support can be attached to the phantom base and a probe path can be developed on the probe support so that when the probe support is attached to the mechanical reference frame, a probe can be passed to the anatomical target in the non-human animal.  
         [0009]     Advantageously, an anatomical target determined or visualized in image scan data can be determined in the physical space of the non-human subject or in the three dimensional stereotactic coordinate system of the mechanical reference frame. Anatomical targets can be calculated with respect to the mechanical reference frame attached to the non-human subject, and the relative positions of anatomical targets and direction of probes or agents to anatomical targets can be determined. An advantage is that quantitative stereotactic study of anatomical targets can be achieved in, for example, neurophysiological study of the brain and brain function of animals. Another advantage is that electrical and chemical activity of targets seen in image data of animals can be determined by directing probes to the targets for the study of function in relation to the positional relationships of anatomical structures in animal organs such as the brain.  
         [0010]     The methods and devices are directed at stereotactic application to non-human subjects which can include apes, monkeys, rats, mice, dogs, rabbits, cats, fish, frogs, pigs, and other creatures. It can also be applied to insects many of which have a firm shell or other structures which can be rigidly or semi-rigidly attached to with a mechanical reference frame.  
         [0011]     The methods and devices can be directed at research into function and features of the anatomy of non-human subjects by stereotactic, quantitative localization of target positions in the subject&#39;s anatomy using application of a mechanical reference frame with image indicia. It also relates to use of imaging machines to produce image data of the anatomy and the image indicia from an imaging indexing element and/or localizer. In one example, the invention can be used for basic research in electrophysiological and neural science by animal experimentation.  
         [0012]     Forms of the stereotactic system and method are disclosed herein in various embodiments. Specific embodiments of mechanical reference frames, image localizers, probe guides, probe guide blocks and guide chambers, phantom bases, arc systems, and computer and graphic displays are disclosed which are suited to the stereotactic system and its use. 
     
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       [0013]     In the drawings which constitute a part of the specification, embodiments exhibiting various forms and features hereof are set forth. Specifically:  
         [0014]      FIG. 1  is a schematic diagram showing a stereotactic system for non-humans.  
         [0015]      FIG. 2  is a schematic diagram showing a stereotactic probe carrier.  
         [0016]      FIG. 3  is a schematic diagram showing a mechanical reference structure with a head ring.  
         [0017]      FIG. 4  is a schematic diagram showing a stereotactic mechanical head ring with fixation posts.  
         [0018]      FIG. 5  is a schematic diagram of a mechanical reference structure with imaging reference index structure attached.  
         [0019]      FIG. 6  is a schematic diagram showing a head ring with indexing reference structure having rods and diagonals and x-ray indicia.  
         [0020]      FIG. 7  is a schematic diagram showing a head ring with ear bar alignment and various skull-clamping positions.  
         [0021]      FIG. 8  is a schematic diagram showing a reference structure attached to a skull with a variety of skull fixation post and rod positions.  
         [0022]      FIG. 9  is a schematic diagram showing a reference structure attached to a skull with various skull fixation positions.  
         [0023]      FIG. 10A  is a schematic diagram showing a skull bone drill and guidance system.  
         [0024]      FIG. 10B  is a schematic diagram showing a skull screw and alignment system.  
         [0025]      FIG. 10C  is a schematic diagram showing a skull screw and pin alignment system.  
         [0026]      FIG. 10D  is a schematic diagram showing a skull anchor and skull screw with a pin fixation system.  
         [0027]      FIG. 11  is a schematic diagram showing a pointed skull pin and drive.  
         [0028]      FIG. 12  is a schematic diagram showing a stereotactic probe guide and arc system on a head ring and skull.  
         [0029]      FIG. 13  is a schematic diagram showing a stereotactic arc system and head ring on a skull.  
         [0030]      FIG. 14  is a schematic diagram showing a probe alignment system with a phantom base.  
         [0031]      FIG. 15  is a schematic diagram showing multi-hole probe guide block attached to a skull and a image-indexing reference structure attached to the guide block.  
         [0032]      FIG. 16  is a schematic diagram showing a sectional view through a guide block and attached indexing graphic reference structure with stereotactic indicia.  
         [0033]      FIG. 17  is a schematic diagram, in sectional view, showing an mechanical reference frame attached to the non-human animal skull with a graphic imaging index reference structure and probe guide block.  
         [0034]      FIG. 18A  is a schematic diagram showing a head post with pointed skull screw.  
         [0035]      FIG. 18B  is a schematic diagram showing a head post with skin punch.  
         [0036]      FIG. 18C  is a schematic diagram showing a head post with skull drill.  
         [0037]      FIG. 18D  is a schematic diagram showing a head post with skull anchoring screws.  
         [0038]      FIG. 19  is a flow diagram showing a process of stereotactic target determination on non-human subjects.  
     
    
     DETAILED DESCRIPTION  
       [0039]     Brain stereotaxy is described, for example, in portions of U.S. Pat. No. 4,608,977; System Using Computed Tomography as for Selected Body Treatments; Russell A. Brown, issued Sep. 2, 1986, and the book  Tumor Stereotaxis  by P. T. Kelly, W. B. Saunders Company, 1991, each of which is incorporated by reference in its entirety. Portions of the Kelly book describe some stereotactic frames that have been designed for use on non-human animals. Examples of non-human stereotactic frames are available from David Kopf Instruments, and they generally relates to brain target determination from bony landmarks on the skull. For example, a method for imaged-based stereotaxy in monkeys is presented in the paper by D. W. Risher, X. Zhang, E. Kostarczyk, A. P. Gokin, C. N. Honda, and G. J. Giesler, Jr. entitled “A method for improving the accuracy of stereotactic procedures in monkeys using implanted fiducial markers in CT scans that also serve as anchor points in a stereotactic frame”, published in the Journal of Neuroscience Methods, Volume 73, Pages 81-89, 1997, which is incorporated by reference in its entirety.  
         [0040]     Referring to  FIG. 1 , in one embodiment, a stereotactic mechanical reference frame includes a mechanical post  1  is fixed directly to the skull S of a non-human animal A. The post  1  is rigidly affixed to the skull S by a screw  4  that is firmly screwed into the bone of the skull S. A stereotactic coordinate frame reference  5  associated with the stereotactic, mechanical reference frame is indicated schematically by the by the Cartesian coordinate axes X, Y, and Z with respect to post  1 . A graphic or indexing reference structure comprising a set of mechanical index markers  7 ,  10 , and  12  is attached to post  1  by rigid arms  17 ,  21 , and  24 , respectively, which can be arranged in a rigid body. The rigid body is attached in a fixed, predetermined position on post  1  by attachment screw  30 . The index markers  7 ,  10 , and  12  can include materials that are detectable positions when the graphic reference structure is imaged in an image scanning machine, such as CT, MRI, x-ray, or other kinds of imaging machines.  
         [0041]     Also shown in  FIG. 1  is an imaging machine  37  which can be, for example, a MRI, CT, PET or other tomographic, volumetric, or planar projective imaging system. The imager  37  produces an image of the anatomy of the non-human animal&#39;s skull S and tissue around and inside the skull S such as the brain indicated by the dashed contour B as well as an anatomical target within the brain such as target T. The imaging system can include a control element  44  which includes electronics, software, and data collection elements to produces image data related to the images from the scanner  37 . The data from element  44  can produce graphic images of the anatomy of animal A as shown schematically by display element  47 . The image of the skull S is shown as contour  51 , the brain B as contour  57 , the target T as position  66 . The index markers on the graphic reference structure, such  7 , 10 , and  12 , are adapted to shown up on the image data from scanner  37  and control unit  44  as image indicia  77 ,  80 , and  82 , respectively. Other embodiments of the graphic reference structure can include more than three index markers to suit scientific purposes and/or the type of imaging data collected by image scanner  37  and control unit  44 .  
         [0042]     The data from control  44  related to the indicia  77 ,  80 , and  82  can be inputted to, controlled by, or managed by computer, software elements, programs, or manual graphic computation element  93 . Element  93  can be used to determine the coordinate position of the target image  66  with respect to the stereotactic mechanical reference frame  1  and the stereotactic coordinate frame  5  associated with the graphic reference structure. The target T can be an anatomical structure, a region or focus of neurological or neurochemical activity, which can be detected by image scanner  37  and associated with target image data related to location  66  on display element  47 . The target indicated by position  66  can be imported into the control  44  and display  47  from another data source  104  such as another image scanner, MEG machine, or EEG system.  
         [0043]     Referring to  FIG. 2 , a probe carrying system  107 , which can also be referred to as an arc system or a stereotactic guidance system, is attached to the post  1 , which is affixed to the skull S as shown in  FIG. 1 . Referring to  FIG. 1 , the rigid indicia structure and graphic reference structure including arms  17 ,  21  and  24 , and markers  7 ,  10  and  12 , has been removed by loosening screw  30 , and replaced by probe carrying system  107  which is secured to post  5  by screw  30  in a predetermined orientation as shown schematically in  FIG. 2 . Referring again to  FIG. 2 , probe guide  112  can be moved on arc  118  over angular ranges indicated by arrow  130  and can be moved over another angular degree of freedom on trunion  124  over an angular range indicated by arrow  140 . The probe carrier  112  can be set to direct probe  157  along a probe path direction to aim at target T as calculated from the image scan data as shown in  FIG. 1 . The probe carrying system can have translational and/or rotational degrees of freedom so that the position of any target T can be achieved by probe carrier from any direction. The degrees of freedom can have quantitative position scales to enable directing a probe, such as  157 , accurately to a target coordinate position with respect to post  1  or with respect to the graphic reference structure of  FIG. 1 . In another embodiment, the probe carrier  107 , indicia structure, and stereotactic mechanical reference frame  1 , or any subsets of these elements, can be integrated into a single, unified apparatus which does not require the separation of these elements. In another embodiment, the stereotactic reference frame  1  can attach to more than one location on the skull S to reduce torques at the interface of the frame  1  and the skull S and to give the affixation greater mechanical stability.  
         [0044]     Referring to  FIG. 3 , an embodiment of a stereotactic mechanical reference frame can include a head ring  170  that can be a rigid structure which encircles the skull S of the non-human animal. The skull S is a schematic shown in  FIG. 3  as the skull of a monkey, for example, the macaca mulatta. The skin of the non-human animal is not shown in  FIG. 3  so that the attachment of head ring  170  to skull S can be simply illustrated. Posts  174 ,  178 ,  182 , and  186  are rigidly attached to the head ring  170 . Attachment rods  190 ,  194 ,  198 , and  202  pass through posts  174 ,  178 ,  182 , and  186 , respectively, and attach to the skull S. The rods can be fixed in the posts to hold the head ring  170  firmly and rigidly to the skull S. In one embodiment, the posts can be unified with, or integrally fixed to the head ring. In another embodiment, each post can be independently adjusted, pre-adjusted and/or fixed in a variety of locations and orientations so that the direction of the attachment rods  190 ,  194 ,  198 , and  202  can be configured to improve the mechanical stability and rigidity of the attachment of the head ring  170  to the skull S. This adjustability can be accomplished, for example, by drilling multiple holes in the head ring  170  such that each post can be attached to the head ring in a number of different positions. For example, in one embodiment of the system in  FIG. 3 , the post  186  can be positioned, oriented, or angulated by different attachment positions to head ring  170 . Bolts  187  and  188  pass from below through holes drilled in head ring  170  and screw into the post  186 . Multiple hole positions such as  189 A and  189 B in head ring  170  enable different attachment positions of post  186  to ring  170 . Other holes, such as  191  and  192 , enable the adjustment of post  174  and rod  190 . Similar adjustment holes on ring  170  accommodate the other posts  178  and  182  orientation and position selection. One advantage of adjustable post and rod positions is that the attachment point of each rod, such as point  203  for rod  202 , can be chosen to suit the particular shape of skull S, to suit the variations in thickness of the skull bone, and/or to suit other scientific needs.  
         [0045]     Referring to  FIG. 3 , the attachment of each pair of post and attachment rod,  174  and  190 ,  178  and  194 ,  182  and  198 ,  186  and  202 , can be configured to attach to the skull at the Left Periorbital Bone Region indicated by shaded region LPB, at the Left Occipital Bone LOB, at the Right Occipital Bone ROB, and at the Right Periorbital Bone Region indicated by shaded region RPB, respectively. The LPB comprises the region near the left ocular orbit of skull S, and can include the left orbital bone itself, the anterior portion of the left zygoma LZA, and the bone of the snout adjacent to the zygoma. The RPB comprises the region near the right ocular orbit of skull S, and can include the right orbital bone itself, the anterior portion of the right zygoma, and the bone of the snout adjacent to the zygoma. The LOB, ROB, LPB, and RPB contain bone which is typically among the heavier bone of the skull S of a monkey, such as the macaca mulatta. One advantage of attaching the head ring  170  by rods fixed to those regions of the skull S is that those regions can comprise heavier bone structures which are less fragile and provide a more stable attachment or anchoring point, thus reducing the chance of displacement of the ring  170  relative to S. Another advantage of the attachment of pin, rods, screws or other hardware to those regions of the skull S is that those regions typically contain bone which is substantially flat or which has small curvature; this quality can facilitate attachment to these locations and make attachment to these locations more stable. For instance a spike is less likely to slip, and a screw is better seated on a flat surface. The attachment rod  194  attached at the LOB and the attachment rod  202  attached at the RPB can be oriented to be on the opposite side of the skull S. This can have the advantage of stable mechanical attachment to the skull S by substantially clamping the skull S between the posts  178  and  186 . Similar opposing clamping can be achieved between opposite posts  182  and  174  related to rods  198  and  174 , respectively, which attach to the skull S at ROB and LPB, respectively.  
         [0046]     In another embodiment, more than four posts and rod pairs can be used on head ring structure  170  to clamp or hold skull S to suit scientific needs. Other attachment points to skull S can be used. In another embodiment, only 3 post and rod pairs can be used on head ring  170  to stably fix head ring  170  to skull S. In another embodiment, only two post-and-attachment-rod pairs can be used on ring  170  to attach to skull S. In examples, the attachment rods can be sharpened, pointed rods that dig into the outer surface of skull S, or screws that can screw into skull S at the contact point, or pins that attach into pre-drilled socket holes in skull S, or forked or cusp-tipped rods that dig in and grip the bony skull.  
         [0047]     In one embodiment, such as that in  FIG. 3 , the opposing attachment rods, such as  190  and  198 , or  194  and  202 , can be are substantially collinear or coplanar to reduce torques and give the affixation of the head ring  170  to the skull S mechanical stability. In another embodiment, the head ring is attached to skull S of a non-human animal, such that there is at least one attachment rod which attaches to the skull S in the LPB or the RPB, and at least one attachment rod which attaches to the skull S in the bone of the occipital region of the skull. For example, in one embodiment, a single post and rod can attach to ring  170  at the rear of skull S and attach near the midline position on the occipital bone.  
         [0048]     Referring to  FIG. 3 , an embodiment of a stereotactic, mechanical reference frame, such as the head ring  170 , is configured to the size and shape of the skull S of the non-human animal. For example, in one embodiment, the skull S is that of a monkey, such as the macaca mulatta, whose typical skulls are smaller than those of typical human beings. In one embodiment, the stereotactic mechanical reference frame, such as head ring  170 , is configured to closely fit the skull of a monkey, such as the macaca mulatta. In another embodiment, the area of the volume surrounded by a stereotactic mechanical reference frame, such as head ring  170 , its posts, such as  174 ,  178 ,  182  and  186 , and its rods, such as  190 ,  194 ,  198 ,  202 , is smaller than that which would practically accommodate the typical human head for the purpose of image-based stereotaxy. In another embodiment, the inner opening of head ring  170  spans no more than 6.3 inches in the direction configured to substantially align with the medial axis of skull S, and not more than 4.6 inches in the direction configured to substantially align with the right-left axis of the skull S. In another configuration, a stereotactic mechanical reference frame is configured so that each attachment rod spans no more than 1 inch between its point of contact at skull S and its point of contact at its stereotactic mechanical reference frame, when the stereotactic mechanical reference frame is attached to skull S of a non-human animal. For example, when head ring  170  is sized so that when it is attached to the skull S of a non-human animal, such as a monkey, such as macaca mulatta, the distance along each rod, from its respective attachment point to its respective post, is not more than 1 inch. For example, head ring  10  is sized so that when it is attached to skull S, the distance between attachment point  203  and post  186  along rod  202  is not more than 1 inch. One advantage of this configuration to the skull size and shape of the non-human animal is an improvement in the mechanical stability of attachment between skull S and the stereotactic mechanical reference frame, such as head ring  170 .  
         [0049]     Referring to  FIG. 4 , a head ring  170 , as described in connection with  FIG. 3 , is attached to the skull S of a non-human animal. The post  178  is longer than the post  174  so that the head ring  170  is substantially parallel to the orbitomeatal plane indicated by the dashed line labeled OMP. Pins  190  and  202  sercure the posts to the skull. The OMP can be defined as passing through any three of the following points: the left auditory meatus LAM, the left occipital bone LOB, and the left infraorbital ridge LIOR. The OMP is typically substantially parallel to the AC-PC line, which passes through the anterior commissure and the posterior commissure in the brain of many non-human animals, and defines one of the principle directions of some animal brain atlases. The posts  174 ,  186 ,  178 , and  182  shown in  FIG. 3  are also configured such that their respective rods have direction which is substantially perpendicular to their respective attachment points in the LOB, ROB, LPB, and RPB. One advantage of this configuration is that the attachment rods can be less likely to slip than they would if they approached the surface of the skull S at more glancing angles.  
         [0050]     Referring to  FIG. 5 , a graphic reference structure or image index structure is attached to the head ring  170  in a predetermined position. The reference structure includes a bottom plate  210  that can be fixed in a known position to ring  170  by securing members, such as screws or clamps, so that the graphic reference structure can be attached and removed from ring  170 . Structures  218 ,  222 ,  226 , and  230  are configured to produce image indicia data when scanned with an image scanner represented schematically by element  234 , so that the coordinates of imaged targets can be determined relative to the head ring  170 .  
         [0051]     The structures  218 ,  222 ,  226  and  230  can, in one embodiment, include a geometric array of rods or channels arranged on the sides of a rectangle, and diagonal rods/tubes arranged on diagonals or in an oblique configuration. For example, structure  218  can have vertical parallel rods  211  and  212 , horizontal parallel rods  213  and  214 , and at least one diagonal rod  215 . The rods can be constructed with materials that are detectable in CT, MRI, PET or other imaging machines. A planar image slice through structure  218  can produce index images or image indicia in the image scan data for that slice corresponding to the intersection of the image slice plane at the parallel and diagonal rods. The image indicia detected for each of the structures  218 ,  222 ,  226 , and  230  can produce sufficient image data to calculate the position of the image slice with respect to the image reference structure  218 ,  222 ,  226  and  230  and thus to the head ring  170 , to which the image reference structure is attached in a known location. In this way, the coordinates of anatomical points or structures detected in the image data and in the scan slice can be determined relative to the structures  218 ,  222 ,  226  and  230  an relative to the head ring  170 . Examples of image reference structures and head rings used in human stereotaxy to determine stereotactic coordinate positions of anatomical targets is illustrated by the CRW stereotactic system produced by Radionics, Inc. of Burlington, Mass., which is described in portions of the book entitled “Handbook of Stereotaxy Using the CRW Apparatus”, edited by D. Thomas and M. Pell, Williams and Wilkins, Co., 1994, which is incorporated herein by reference in its entirety.  
         [0052]     Also shown in  FIG. 5  is image scanner  234 , which can be MRI, CT, PET, x-ray or other tomographic, volumetric, or planar imaging system. The image scanner is associated with element  240  can include controls, electronics, graphic display, computational systems, manual computation, mechanisms to associate scan data from  234  with other scan data, and other systems and methods related to collecting image data, producing scan images, and computing the coordinates of targets relative to the head ring  170 .  
         [0053]     Referring to  FIG. 6 , one embodiment of an index reference structure  246  is attached to the head ring  170  in a known position. For example, the index reference structure  246  can be similar to that described above. The index reference structure  246  can include a bottom plate  248 , a top plate  244 , and parallel plus diagonal rod structures  252 ,  256 ,  260 ,  264  and  268  which are configured to produce image indicia data when scanned with an image scanner like that shown in  FIG. 5 . Image indicia data produced by structures  252 ,  256 ,  260 ,  264  and  268  in sagittal, coronal and axial planar image scans can be used to determine the coordinates of imaged targets. The index reference structure in  FIG. 6  also includes reference elements  272 A,  272 B,  272 C and  272 D;  278 A,  278 B,  278 C and  278 D;  284 A,  284 B,  284 C and  284 D; and  290 A,  290 B,  290 C and  209 D which can produce image indicia when scanned by a projective x-ray apparatus, represented schematically by an x-ray emitter  294 , detector  298 , and control element  302 . The indicia are configured so that the coordinates of anatomy and implanted objects in and around the skull S which are visible when scanned one or multiple times by x-ray imaging scanner comprising  294 ,  298 , and  302 . This system and method can be used, for instance, to confirm the location of electrodes, probes, needles, or other objects that can be imaged by an x-ray scanner, which have been implanted in and about the skull S of a non-human animal. Examples of the use of x-ray visible structures with index markers such as those shown in the embodiment in  FIG. 6  can be found in the CRW Handbook reference described above.  
         [0054]     Referring to  FIG. 7 , the head ring  170  attached to the skull S of a non-human animal is shown from a top view. In different embodiments, different subsets and combinations of types and locations of attachment elements can be used to affix the head ring  170  to the skull S, and  FIG. 7  shows some example embodiments. Rod  306  passes through post  310  and attaches to the skull S in the Left Periorbital Bone Region LPB. Rod  314  passes through post  318  and attaches to the skull S in the Left Zygomatic Arch LZA. Ear bar  322  passes through post  326  and is seated in the Left Auditory Meatus LAM. Rod  330  passes through post  334  and attaches to the skull S in the Left Occipital Bone LOB. Rod  338  passes through post  342  and attaches to the skull S in the Right Occipital Bone ROB. Ear bar  346  passes through post  350  and is seated in the Right Auditory Meatus RAM. Rod  354  passes through post  358  and attaches to the skull S in the Right Zygomatic Arch RZA. Rod  362  passes through post  366  and attaches to the skull S in the Right Periorbital Bone Region RPB.  
         [0055]     Referring to  FIG. 7 , the head ring  170  has an inner lateral opening with width W. It can be advantageous to have W be as small as possible and yet still comfortably accommodating the skull size and skin configuration of the animal such as a monkey. This can increase the stability of a placement of ring  170  on skull S because the posts  310 ,  334 ,  342 ,  362 , and rods  206 ,  330  and  362  can be positioned as close to the animal&#39;s head and as short a distance from the skull S as is practical. Shorter distances of the fixation element can improve stability and vulnerability of fixation of ring  170  to the skull S. For small monkey skulls, a ring  170  with W less than 8 centimeters (cm) is desirable. For small-to-medium monkey skulls, a ring  170  with W less than 10 cm is desirable. For medium monkey skulls, a ring  170  with W less than 12 cm is desirable. For medium-to-large monkey skulls, a ring  170  with W less than 14 cm is desirable. For skulls of large monkeys, or greater non-human apes, a ring  170  with W less than 16 cm is desirable. For tiny monkeys, such as squirrel monkeys, a ring  170  with W less than 6 cm or 7 cm is desirable.  
         [0056]      FIG. 8  shows schematically, from the top view, one embodiment of the head ring  170  attached to the skull S of a non-human animal. In different embodiments, different subsets and combinations of types and locations of attachment elements can be used to affix the head ring  170  to the skull S. In different embodiments, each post can be independently adjusted, pre-adjusted and/or fixed in a variety of locations and orientations. Attachment rod  374  associated with post  378  attaches to skull S at a place on the snout bone SB. Attachment rod  386  associated with post  390  attaches to skull S at a place on the left superior orbital ridge LSOR. Attachment rod  402  associated with post  398  attaches to skull S at a place on the left zygomatic arch LZA. Attachment rod  406  associated with post  410  attaches to skull S at a place on the left occipital bone LOB. Attachment rod  418  associated with post  414  attaches to skull S at a place on the medial occipital bone MOB. Attachment rod  430  associated with post  422  attaches to skull S at a place on the right occipital bone ROB. Attachment at the left cranial vault LCV and right cranial vault RCV can be accomplished with post  408  and post  433 , respectively, with rods, such as  431  for post  433 . Attachment rod  434  associated with post  438  attaches to skull S at a place on the right orbital ridge ROR. Attachment rods  442  and  454 , respectively associated with post  446  and  450 , attach to the skull at places in the right periorbital region RPB and RPB 2 , respectively. Attachment rod  462  associated with post  458  attaches to skull S at a place in the medial periorbital bone regions MPB which comprises the bone between the sockets and the ridge of the snout. The posts, such as  378  and  390 , can be attached in one example beneath ring  45  and in another example above the ring  458  as viewed in  FIG. 8 .  
         [0057]      FIG. 9  shows schematically, from the front view, one embodiment of the head ring  170  attached to the skull S of a non-human animal. In different embodiments, the posts associated with attachment rods can have different heights above or below the head ring  170 . In different embodiments, the attachment rods can attach to the skull S and/or the post at different or multiple heights above or below the head ring  170 . One embodiment of a post  458 , for example, can have multiple holes through which rods  462 ,  466  and  470  can pass. In another embodiment different types of attachment rods can pass through different holes in the same or different posts to suit scientific needs. Attachment rods  462 ,  466  and  470  are attached to post  458  to attach the head ring  170  to the skull S at a location on the left occipital ridge LOR and at two locations in the left periorbital bone region LPB and LPB 2 , respectively, and rods  474 ,  478  and  482  attach the head ring  170  to the skull S at a location on the right superior orbital ridge RSOR, the right zygomatic arch RZA, and the right periorbital bone region RPB, respectively.  
         [0058]      FIGS. 10A, 10B ,  10 C and  10 D show, in cross-section, examples of elements that can be involved in attachment of a stereotactic mechanical reference frame to the right zygomatic bone RZB of skull of a non-human animal. In other embodiments, these elements can be applied to other regions of the skull S, such as the left and right periorbital bone regions, the occipital bone region, the snout bone, the temporal bone, and other bones of the skull S.  
         [0059]     Referring to  FIG. 10A , a drill  498  passes through bushing  490  seated in or aligned in hole  492  in post  486  that can be one or several posts attached to head ring  170  as, for example, described in the  FIGS. 5, 6 ,  7 ,  8  or  9 . The drill  498  drills a hole  494  in surface of the right zygomatic bone RZB of the skull of a non-human animal. Hole  494  can serve as a pilot hole for a skull screw, a seating hole for an anchoring plug or button, or a positioning burr hole for use in attaching and/or registering a stereotactic mechanical reference frame to skull S. One advantage of passing the drill through the hole in an attachment post  486  is that the drilled hole  494  is aligned with any attachment rod which passes through the same hole in attachment post  486 . In another embodiment, hole  494  can be drilled without passing through an attachment post.  
         [0060]     Referring to  FIG. 10B , a screw driver or wrench  506  passes through bushing  502 , seated or guided in post  486  which is attached to head ring  170 , to place screw  510  into hole  494  in surface of the right zygomatic bone RZB of the skull of a non-human animal. In another embodiment screw  510  can be screwed into the skull without the use of a pilot hole and/or without passing the screwdriver through post  486 . In another embodiment hole  494  can be tapped before screw  510  is placed in it. The tools and steps illustrated in  FIG. 10B  can be used following the steps in  FIG. 10A .  
         [0061]     Referring to  FIG. 10C , an attachment rod  518  passes through guide hole  492  in post  486  which is attached to head ring  170 . The rod  518  has a distal tip  519  that is configured to seat in, lock in, screw into, align in, or attach to a socket or attachment element in screw  510  that is rigidly fixed to the right zygomatic bone RZB of the skull of a non-human animal. Biocompatible glue, such as methyl-methacrylate, indicated by hatched region  514 , can adhere or mechanically lock or secure screw  510  to the skull. In another embodiment glue  514  can be omitted. One advantage of glue  514  is that it can provide additional mechanical stability to the attachment of screw  510  to the skull. The end  519  of rod  518  and the head of screw  510  can be configured to attach to each other snugly. Attachment rod  518  can be held rigidly to post  486 , for example, by clamping it with screws  519  and/or  520  which screw into threaded holes in attachment post  486  to press against rod  518 . Depth stop  522  can be attached to rod  518  and mark or set the position of rod  518  in post  486 . One advantage of marking this position is that it can be used for the purpose of a repeat fixation method, in which the head ring  170  associated with post  486  can be repeatedly removed and attached to skull in the same position. By using a depth stop such as  522  that can be clamped on rod  518 , and providing such depth stops on the rods in one or several head posts on the ring, a refixation of the rods, such as  518 , in the screws, such as  510 , can repeatedly attach the ring on the skull in the same position.  
         [0062]     One advantage of passing screwdriver  506  through the hole in an attachment post  486  is that the screw  510  can be aligned with attachment rod  518  which later passes through the same hole in attachment post  486 . One advantage of pre-drilling hole  494  as a pilot hole for screw  510  is that it helps align screw  510  with attachment rod  518 . In one embodiment, attachment rod  518  and/or screw  510  can be configured to attach to each other snuggly when they are aligned in this manner. One advantage of this is that attachment rod  518  and screw  510  attach to each other rigidly. Another advantage of this is that attachment rod  518  and screw  510  can be repeatedly separated and attached in the same position. In another embodiment, the attachment rod  518  can attach directly to bone hole  494 . The drill hole  492  and the tip  517  of rod  518  can be configured to match each other and provide desired repositioning of the rod  518  and thus head post  486  and head ring  170  to the skull S.  
         [0063]     Referring to  FIG. 10D , attachment rod  524  is configured to attach to bushing  526 . Bushing  526  is adhered to skull and additional screws  534  and  538 , which are themselves attached to skull, by glue which is indicated by the hatched region  530 . In other embodiments, one, two, three or more additional screws can be placed in skull and attached to bushing  526  with glue  530 . The surface of bushing  526  can be non-smooth to improve adhesion, mechanical locking and/or securing to glue  530 . In another embodiment bushing  526  can have a smooth or partially smooth surface. Bushing  526  and/or attachment rod  524  can be configured to attach to each other rigidly. For example, rod  524  can have a shouldered tip  525  that fits snuggly into a hole in bushing  526 . Bushing  526  can fit into bone hole  494  by means of a distal tip or shoulder end that fits snuggly into bone hole  494 . This has the advantage that bushing  526  is attached to skull more stability. Attachment rod  524  can be held rigidly to post  486 , for example, by clamping it with screws  519  and/or  520  which screw into threaded holes in attachment post  486  to press against rod  524 . Depth stop  522  can be attached to rod  524  and mark or set the position of rod  524  in post  486 . In another embodiment, bushing  526  can be placed without the use of a bone hole. In one embodiment the bushing  526  can be made out of plastic, or some other material which suits scientific needs such as that of causing small or vanishing artifact when scanned by fMRI, MRI, DTI, CT, PET, MEG, EEG, and other scanning methods.  
         [0064]     Referring to  FIG. 11 , from the top view, one embodiment of an attachment rod  546  passes through post  542  attached to head ring  170 , and attaches to the right zygomatic bone RZB of the skull of a non-human animal. Attachment rod  546  has a pointed, sharpened end  550  which digs into the skull at point  552 . The attachment rod is  546  has a threaded region  558  and passes through a threaded hole  564  in post  542 . Attachment rod  546  comprises element  570  which is configured to accept a driver or wrench. In one example, end element  570  comprises a slot which can accept a screwdriver so that rod  446  can be tightened into its skull attachment point  552 .  
         [0065]     Referring to  FIG. 12 , a stereotactic guidance system is attached to head ring  170  for the placement of probes into the skull S of a non-human animal. By reference, the CRW system for human stereotaxy includes a stereotactic guidance arc which attaches to a head ring adapted for human heads. This is described in the reference on the CRW stereotactic system described above. One embodiment of a stereotactic guidance system includes a bottom plate and rail  660 , which attaches to head ring  170  in a pre-specified, known location with attachment screws  664  and  668 . Slider  676  slides along rail  660  and is configured to provide one translational degree of freedom to the stereotactic guidance system, and rail  660  is ruled with position scale markings  662  to show the coordinate along that degree of freedom. Upright  672  slides through slider  676  to provide a different translational degree of freedom to the stereotactic guidance system, and upright  672  is ruled with position scale markings  674  to show the coordinate along that degree of freedom. Horizontal rail  680  is attached to the top of upright  672 . Trunion  684  slides along horizontal rail  680  to provide a third and different translational degree of freedom to the stereotactic guidance system, and horizontal rail  680  is ruled to show the coordinate along that degree of freedom. Trunion  684  rotates around horizontal rail  680  to provide a rotational degree of freedom to the stereotactic guidance system. Trunion  684  can be angularly ruled with angle degree markings, such as  685 , to show the angular coordinate along that degree of freedom. Arc  688  is attached to trunion  684  and is shaped as a portion of a circular ring or arc. Slider  692  slides along arc  688  to provide another, different rotational degree of freedom to the stereotactic guidance system. Arc  688  can be angularly ruled with angle degree markings, such as  689 , to show the angular coordinate along that degree of freedom. Slider  692  can include a probe carrier which holds an electrode, probe, needle or delivery device  696 . Slider  692  is configured to allow probe or electrode  696  to be advanced to a specified depth through burr hole  700  in the skull S of a non-human animal to either hit or pass through target T in the head of the non-human animal. The stereotactic guidance arc has three degrees of translational freedom and two degrees of rotational freedom so that probe or electrode  696  can be directed at target T from any direction. The stereotactic guidance arc can be configured to direct probe  696  to target T by using the coordinates of target T relative to the head ring determined using a graphic reference structure and image scanner, such as those shown in  FIG. 5 . Probe  696  can be associated with system  704  which can have data collection and/or electrical signal generation functions configured to suit scientific needs. For example, probe  696  can have electrode, or agent delivery tubes, or bio-activity sensors which are cooperatively connected to external apparatus  704  by connection  705  to deliver energy, or bio-agents, or drugs, or image tracer agents, such CT or MRI contrast agents, such as Magnesium, for study of the brain anatomy or function at target T or multiple target regions. Probe  696  can be stimulation, recording, or lesioning probe/electrode, and  704  can provide accompanying electronic apparatus, control, computing, or storage. Probe  696  can also be placed using data collected as it is advanced; one advantage of this is that specific types of neurons or tissue can be targeted in the vicinity of a target T.  
         [0066]     Referring to  FIG. 12 , an embodiment of a stereotactic guidance system comprises parts  708 ,  712 ,  716 ,  720 ,  724 ,  728 ,  732 , and  736 . Rod  736  slides along slider  732  and attaches to probe array plate  740  so that the probe array plate can be advanced toward skull S. Probe array plate  740  can be directed to any location, from any angle using the Stereotactic guidance system; one advantage of this is that the probe array plate can be oriented to facilitate its attachment to skull S. Probe array plate  740  comprises a grid of holes which are configured to hold probes, such as probe/electrode  744 . The Stereotactic guidance system can orient the probe plate array  740  so that probes held by it can be directed at pre-specified targets in skull S. For example, probe  744  is advanced to hit target TT. The length D of probe  744  above the probe array plate  740  and the configuration of the stereotactic guidance arc can be used to advance probe  744  to hit target TT. Probes held by array  740  are connected to element  748  which comprises agent injection, bio-agent detection, image enhancement injection, ablation devices or agents, control, signal generation, and/or data collection functions, such as stimulation or recording from the targets associated each probe in the array  740 .  
         [0067]     In other embodiments, the stereotactic guidance system guides the placement of other types of probes, each with a specific control and/or data collection system, at pre-specified targets in the skull S of a non-human animal. Other types and configurations of probe/electrode carrier can be attached to or reference to the head ring  170  in accordance with the present invention for use in image-scan-guided stereotaxy in non-human animals. For example, articulated arms, robot arms or devices, optically-coupled navigator devices, or magnetically or electro-magnetically tracked navigator devices can be devised by those skilled in the art. Examples of such guidance systems are illustrated in portions of the text on stereotaxy entitled “Stereotactic and Function Neurosurgery”, edited by Philip Gildenberg, M. D., and Ronald R. Tasker, M. D.; 1998; McGraw-Hill Company, which is incorporated in its entirety by reference.  
         [0068]     Referring to  FIG. 13 , another embodiment of a stereotactic guidance system  770  is shown, which can direct a probe  780  at target T at any location in the head and/or skull S of a non-human animal, from any direction. Stereotactic guidance system  770  includes a slider  790  in the shape of a portion of a circular arc which is attached at both of its ends to the rest of the guidance system  770 . One advantage of this configuration is that any target location T in the skull S can be achieved by the stereotactic guidance system  770  when attached to the head ring  170  in a single, fixed and known position. The stereotactic guidance system  770  also includes a base  785  which substantially surrounds the skull S. In another embodiment, the base  785  can completely surround the skull S. One advantage of this configuration is mechanical stability.  
         [0069]     Referring to  FIG. 14 , shown in partial, sectional view, one embodiment of a stereotactic guidance system can be attached to one embodiment of a phantom base for the purpose of achieving one or more targets in the head of a non-human animal with a probe, needle or delivery device  800  held in an probe array plate  804 . One embodiment of a probe array plate  804 , shown in cross-section, includes a plate containing one or more holes, such as hole  888 , which are configured to hold electrodes, needles, probes, or other delivery or monitoring devices. The embodiment of a stereotactic arc shown in  FIG. 14  includes base  808 , slider  812 , upright  816 , trunion  820 , horizontal rail  824 , arc  828 , slider  832 , and bar  836 . It is analogous to those embodiments shown in  FIGS. 12 and 13 . The phantom base includes a ring-shaped top plate  840  which can have a shape similar to its corresponding head ring, an example of which is head ring  170 . The embodiment of a phantom base shown in  FIG. 14  includes a bottom plate  844  and uprights  848  and  852 . The phantom base is attached to the stereotactic guidance system in a pre-specified location by attachment screws  876  and  880 . The phantom base comprises a pointed rod  872 , called the phantom base pointer, whose tip can be moved and fixed at any location T1 achievable by the stereotactic guidance system. Rod  872  slides vertically through slider  868  to provide the pointer  872  with one degree of translational freedom. The rod  872  is ruled to show the coordinate of its tip  874  along that degree of freedom. The slider  868  slides horizontally along rail  856  to provide the pointer  872  with another translational degree of freedom. The rail  856  is ruled to show the coordinate of the tip of rod  872  along that degree of freedom. The rail  856  slides along rails  860  and  864  horizontally in the direction perpendicular to the plane of the page along rails  860  and  864 , to give the phantom base one degree of translational freedom. The rails  860  and  864  are ruled to give the coordinate of the tip  874  of rod  872  along that degree of freedom.  
         [0070]     The scales on the components of the phantom base, which in this embodiment are pointer  872  and the rails  856 ,  860  and  864 , are configured so that the location of the point tip can be set relative to the coordinate frame of the phantom base. Since the phantom base attaches to the stereotactic guidance system in a known position, the tip of the pointer  872  can be set to a pre-specified location T1 relative to the stereotactic guidance system. Therefore, since the stereotactic guidance system attaches to the head ring  170  in a known position, the tip  874  of the pointer  872  can be set to the 3-D stereotactic target coordinates of a coordinate location of an anatomical target in the skull S of a non-human animal to which the head right  170  is attached. For example, such as anatomical target can be that specified by T in  FIG. 1  and  FIG. 12 . The 3-D coordinates of targets T1 can have been determined from image data of anatomy and index indicia. The stereotactic guidance system can be configured to orient probe array plate  804  so that electrodes, such as  800 ,  830  and  892 , can achieve one or more anatomical target locations, such as T1 and T2, when electrode are placed through the array plate  804  on the phantom base where the coordinates of T1 and T2 have been set. The stereotactic guidance system can also orient the array plate  804  so that it can be attached to the skull S. For example, plate  804  can be separated from slider  836  after probe placement and fixedly attached to the skull S of an animal during the surgical phase of the procedure.  
         [0071]     Referring to  FIG. 14 , in this embodiment, the holes in array plate  804  are cylindrical each with a diameter greater than that of cannula  904 . The probe  800  is configured to pass through and be held by the cannula  904 ; therefore, the probe  800  can pass through array plate  804  in a variety of orientations. The pointer  872  is set to achieve the target location T1. The stereotactic guidance system is configured to orient the array plate  804  so that probes, such as  800 ,  830  and  892 , passing through it can achieve targets, such as T1 and T2. The probe  800  and its cannula  904  are oriented and advanced to achieve target coordinate location T1 so that the cannula  904  passes through a hole in the array plate  804 . The cannula  904  can be fixed in this orientation to the array plate  804  by glue, indicated by blacken region  884 , which can enter the hole in the array plate. Cannula  896  can be fixed to plate  804  by glue  900  so that electrode  892  achieves target T2. The position of each probe,  800  and  892 , can be noted by measuring and/or marking the exposed length, D1 and D2 respectively, when it achieves its target coordinate location, T1 and T2 respectively. The probes  800  and  892  can be removed from the cannula  904  and  896  fixed to the array plate  804 , and the phantom base can be detached from the stereotactic guidance system. The stereotactic guidance system can then be attached to the head ring  170  on skull S, as shown in  FIG. 12  and  FIG. 13 . After this, electrodes  800  and  892  can be replaced in their respective cannula  904  and  896  in the same positions, so that the electrodes achieve anatomical targets at the coordinate positions associated with locations T1 and T2. One advantage of this configuration and method is that more than one target coordinate location, such as T1, T2 and others in the vicinity of T1 and T2, can be achieved with high accuracy by multiple probes, such as  800  and  892 , held in the array  804 .  
         [0072]     Referring to  FIG. 14 , in another embodiment, cannula  831  is guided in hole  833  in plate  804 . The probe  830  can be guided in the cannula  831 . Close tolerance between the diameters of hole  833 , cannula  831 , and probe  830  can provide sufficient accuracy to enable probe  830  to approach target position T1 at pointer tip  874  with sufficient accuracy to suit scientific needs with the need to fix probe and cannula with glue as in the samples of probes  800  and  892  just as shown. The coordinates of T1 can be set both on arc slides and phantom vases sliders so that the tip of probe  830  should approach and touch tip  874  at a prescribed advancement distance of  830  inside guide hole  833 . This can provide a check of the correctness of the stereotactic coordinate settings associated with target T1 prior to placing the arc on the head ring such as  170  and advancing the probes into the animal&#39;s brain to achieve an image-based calculated target position such as T in  FIG. 12 .  
         [0073]     Referring to  FIG. 15 , a mechanical reference structure includes a probe guide block  920 . Block  920  is rigidly attached to the skull S of the non-human animal. The attached includes skull screws such as  925 ,  927  and  929  which are screwed into the skull bone. Cement or adhesive  934  attaches to the heads of the skull screws  925 ,  927  and  929 , and also attaches to the side edges or bottom of block  920 . In one example, block  920  can have a multiplicity of guide holes, such as hole  937 , through which a probe shaft such as element  941  can pass and can penetrate into the animal&#39;s brain BR. A chamber  945  is attached to block  920 , and in one example, can be a box-like structure that can serve to reduce infection around the block  920  and probe  941 , and can mechanically protect the probe  941 . A graphic reference structure  950  can be rigidly attached to the chamber  945  by screws such as  953 . The structure  950  has rod and diagonal graphic indicia structures such as  960 ,  970  and  980  on the top and left and right sides. The rods and diagonal element of structures  960 ,  970  and  980  can provide image scan index data similar to the examples described in  FIG. 5  and  FIG. 6 .  
         [0074]     An image scanner  987  such as a CT, MRI, PET or other tomographic or volumetric scanner, can produce image data in one or more scan slices, such as in plane  990 , which produces index data corresponding to the plane&#39;s  990  intersection with the rod and diagonal structures of elements  960 ,  970  and  980 . The image and indicia data can be processed by computer  994  and displayed on display  997 . The data from scanner  987 , with anatomical and graphic indicia data from structure  950 , can enable calculation of target coordinates of anatomy seen in slice  990  with respect to graphic structure  950 , that is in coordinates of a three dimensional coordinate system indicated by the axes X, Y, Z defined with respect to the structure  950 . Structure  950  can be mechanically fixed in a known position with respect to block  920  so that the position of holes, such as holes  937 , can be determined relative to structure  950 . In this way, the path of probes such as  941 , can be determined relative to localizer  950  and also with respect to the animal&#39;s anatomy seen in the image slice data. Multiple scan slices, such as in plane  990 , can be gathered to give a volumetric determination of the coordinate relationship of the holes in block  920  and the anatomy such as brain BR. In the this way, the position of anatomy achieved by a probe that is passed through any hole in the block  930  can be calculated as a function of the depth of penetration of a probe through the hole.  
         [0075]     Referring to  FIG. 16 , a planar sectional view through the anatomy of the body B and the index structure  1000  is shown schematically. In one example, this can represent a tomographic planar image data slice including skull S and skin SK, such as in plane  900 , as shown in  FIG. 15 . The sectional image of block  920  in  FIG. 15  is shown in  FIG. 16  as element  1010 , and the channel hole  937  in  FIG. 15  appears as an image channel  1015  in  FIG. 16 . The slice image of chamber  945  is shown as  1025 . The graphic indicia from localizer element  960  appears in  FIG. 16  as image spots  1031 ,  1033  and  1035  for the rods of structures  960 ; spots  1045 ,  1049  and  1052  for the rods of structure  970 ; and spots  1057 ,  1061  and  1063  for the rods of structure  980 . In the image slice plane represented by the image of  FIG. 16 , there can be an associated two dimensional coordinate system represented by the axes X′,Y′. Each point in the image, such as the centers of the index spots  1031 ,  1033 ,  1035 ,  1045 ,  1049 ,  1052 ,  1057 ,  1061  and  1063 ; the hole location  1015  (if it is visible in the scan), and any visible target point, such as point T, can have a definable coordinate location in X′,Y′ space. A transformation can be made between X′,Y′ space and the X,Y,Z coordinate space of the structure  950 .  
         [0076]     One advantage of the chamber such as  945  and guide block  920  is that they can remain on the animal anatomy for long periods. For example, in brain research, electrodes like probe  941  can be placed in a brain for months or more, and electrical recording can be done for long-term brain experiments. The chamber  950  can protect the electrodes and inhibit infection. An advantage of the localizer  950  attached to chamber  945  is that multiple and long-term repeat image scans can be done during experiments to monitor probe position and/or determine new targets for new probe placement.  
         [0077]     Referring to  FIG. 15 , in one example, the rods and diagonals of structures  960 ,  970  and  980  can be tubes or channels filled with a medium or solution, such as gadolinium solution, that is visible in an MRI scan. Referring to  FIG. 16 , if scan  987  is an MRI image plane, the index points such as  1031 ,  133 ,  1035 ,  1045 ,  1049 ,  1052 ,  1057 ,  1061  and  1063  will appear as dots or ellipses and their X′,Y′ coordinates can be determined. The brain BR of the animal&#39;s body B will also be visible in the MRI scan and a target T, accessible by path  1067 , can be chosen and it&#39;s X′,Y′ coordinates determined. Referring to  FIG. 15 , the plane of scan  990  can be calculated from the index points, and the position of the hole, such as  937  in grid  920 , which produces the best path to target T can be determined. The scan plan  990  can be aligned or non-aligned with the sides or axes of grid  930  and structure  950  to suit the research needs. Many slice images such as  990  can be acquired, and a full three dimensional reconstruction of the position of grid  920  relative to the localizer  950  and relative to the brain BR can be computed by  994  and displayed on element  997 . Paths through one or more holes like  937  in grid  920  can be determined, and the position and depths of probes such as  941  can be planned to achieve one or more target positions in the anatomy. In another example, scan  987  can be a plane from CT, PET or another type of tomographic imaging, and the rods and diagonals of structures  960 ,  970  and  980  can be tubes or channels filled with a medium or solution configured so that they are visible in scan  987 .  
         [0078]     One advantage for brain research is that targets that are visible in MRI or other image scans can be selected and can be achieved with probes in a calculable, accurate, and proscriptive way using the mechanical reference frame, graphic localizer, and probe guide system show in the  FIGS. 1 through 16 . In one example, microelectrodes can be accurately placed in desired position in the brain structures based on high resolution MRI or other types of imaging. Confirmation of probe position can be done by repeat scanning using the graphic localizer indicia. Desired probe paths can be selected before insertion by quantitative image scan data. Data from multiple images sources such as MRI, CT, x-ray-, PET and electrical or chemical studies can be combined in one quantitative coordinate basis such as the X,Y,Z coordinate system associated with a structure or a frame for cross-comparison and sequentially timed studies of brain activity.  
         [0079]     Referring to  FIG. 17 , a head ring is attached to an animal&#39;s skull S in body B.  FIG. 17  is a schematic diagram in sectional view though the device and anatomy. There are posts, such as  1104  and  1106 , which are below the head ring and skull anchors, such as  1111  and  1114 , which pass through the post to anchor the head ring to the skull bone S. A probe guide  1117  is attached to the head ring  1101  and has multiple holes, such as  1117 , that can provide access into targets such as T in brain BR by probes such as  1124 . In one example, probe  1124  can be an electrical recording probe that is attached to electronic circuit  1131  to stimulate or record brain activity near T. Chamber  1145  encloses one or more probes in carrier  1117 . One purpose of the chamber  1145  can be to protect enclosed probes in carrier  117  from being hit. Another purpose of the chamber  1145  can be to act as a barrier against infection. As seal  1151  and  1157  can also prevent dirt and infection from entering the region of the bone and skin opening BO. The graphic reference structure  1161  can be permanently fixed to chamber  1145  or in another case can be attached and then removed from  1145 . Index reference structure  1161  has imaging indicia, such as rods and diagonal structures similar to those shown in other embodiments herein. In a tomographic image slice through the localizer  1161 , the indicia will be detected as spots such as  1166 ,  1118  and  1170 . From these indicia images, targets such as T can be determined relative to localizer  1161  and relative to frame  1101  and grid  1117 , so that desired probe holes, such as hole  1129 , and probe paths can be chosen to reach desired target anatomy.  
         [0080]     Referring to  FIG. 18A, 18B ,  18 C and  18 D, a series of instruments are shown schematically that can be passed through one more head posts, such as  1104  in  FIG. 17 , to secure a mechanical reference frame to the rigid anatomy of a non-human subject. Referring to  FIG. 18A , a portion of a head post  1121  is shown in sectional view having a threaded hold  1208 . A screw  1201  is threaded in hole  1208 , and it has a pointed tip  1204 . Tip  1204  can penetrate soft tissue SK, which in one example can be the scalp. The point  1204  can then dig into the bone anatomy portion S, which can be the skull. In an embodiment involving a head ring such as in  FIGS. 3, 4 ,  5 ,  6 ,  7 ,  8 ,  9 ,  12 ,  13  and  17 , multiple sharpened screws like  1201 , through multiple head posts, can rigidly fix the head ring to the animal&#39;s skull.  
         [0081]     Referring to  FIG. 18B , a skin punch is shown passing through the hole  1208  of post  1207 . In one example, with head ring first secured to the skull with screws such as in  FIG. 18A , each screw could be sequentially removed, and a skin punch  1214  can be passed through each post, such as post  1207 . The tip  1217  has a sharpened edge so that it can core into or punch a core of skin SP from scalp SK to produce a hole in skin SK down to the bone S.  
         [0082]     Referring to  FIG. 18C , a drill  1221  can then be passed through hole  1208  after the skin punch core is removed. Drill tip  1224  can make a hole  1227  in skull S.  
         [0083]     Referring to  FIG. 18D , a shouldered screw  1231  can be threaded into hole  1208  in post  1207  after the hole  1227  has been made as in  FIG. 18C . The screw  1231  has a cylindrical tip  1234  which fits into hole  1227 , and it has a shouldered edge  1237  which can be driven to the outer edge of bone S to stabilize the penetration of screw  1231  against the bone S. Slot  1241  on the distal end can accommodate a tool to advance screw  1231  into hole  1227  until shoulder  1237  reaches bone S.  
         [0084]     For a head ring such as shown in the figures herein, sequential application of the tools shown in  FIGS. 18A, 18B ,  18 C and  18 D, one head post after another, can enable the head ring to fix the skull for long periods, as for example, to enable long-term experiments to be performed on an animal subject. An advantage of such as set of fixation instruments and such a method is that the final screw anchors such as  1231  can produce relatively little sustained inward force on the skull bone S to prevent bone erosion and/or necrosis. Also the tip and shoulder provide stable anchoring to the bone S for each post for long term, reliable, fixation position of a mechanical reference frame to the animal&#39;s skull.  
         [0085]     Referring to  FIG. 19 , a flow chart is shown that illustrates a method of treating the interior of a body at a target location. A mechanical reference frame, such as in one example a head ring, is fixedly attached to the skull of a non-human animal (step  1301 ). This can be done by attaching or positioning head posts, screws, rods, repeat localizer buttons, or a guide block directly to the skull bone as illustrated in the embodiments of  FIGS. 1 through 16 . An index reference structure is then attached to the mechanical reference frame in a defined mechanical position (step  1307 ). The index reference structure can have rod and diagonal elements, spots, dots, markers, spheres, geometric shapes, and/or other graphics indicia that are constructed of a material that can produce detectable indicia data in image data when the index reference structure and the non-human animal&#39;s anatomy are imaged by an imaging machine, such as CT, MRI, PET, MEG, EEG, x-ray, infrared, impedance, and other imaging machines. The non-human animal with the mechanical reference frame attached to its skull and the index reference structure attached to the mechanical reference frame, is then imaged by the imaging machine (step  1312 ). This produces image data corresponding to the non-human animal&#39;s anatomy and the indicia of the index reference structure. From the image data and from the geometry of the indicia of the index reference structure, the coordinate position relative to the index reference structure and thus the mechanical reference frame, of anatomical targets or regions detected in the image data can be computed and/or graphically determined (step  1314 ). A probe path can be computed froma desired direction relative to the animal&#39;s anatomy and in the coordinate system of the mechanical reference structure, the index structure, and/or the probe guide (step  1316 ). The index reference structure can be removed from the mechanical reference frame, and the mechanical reference frame can be removed from the skull of the non-human animal (step  1321 ). Alternatively, the mechanical reference frame can be kept on the skull of the non-human animal. If the mechanical reference frame is removed, it can be constructed so that it can be repeatedly, and with sufficient accuracy to suit scientific needs, repositioned or refixed on the skull of non-human animal (step  1321 ). For example, the surgical procedure of placing probes in the non-human animal brain can occur days or months after image data acquisition, and in that case, repeat fixation of the mechanical reference frame to the animal is desirable. A probe guide apparatus such as stereotactic guidance system or digitized navigator can be attached to and/or referenced mechanically to the mechanical reference frame an/or phantom base (step  1324 ). Alternatively, the mechanical reference frame can have built-in or integral probe paths such as guide holes in a guide block. Probe paths and probe positions can be established on the probe guide to hit target determined in step  1314 . If a phantom base is used, correction to probe path and positions can be set up and fixed on a probe carrier or plate to enable a probe or probe array to be established. The probe guide can be fixed to the mechanical reference frame, and the probes can be passed into the brain or spinal region of the non-human animal so that those probes are positioned accurately at targets determined by imaging data. A probe plate, such as a probe array plate which can hold implanted probes, can be fixed to the animal&#39;s skull with glue and detached from the probe guide to leave the probes in the brain. Using the localizer illustrated in  FIGS. 1, 5  and  6 , confirmational lateral and/or frontal x-rays and/or CT, MRI, and/or PET images can be done (also step  1324 ) to confirm or redetermine the position of probes and their tip positions in the animal&#39;s anatomy after surgery or a subsequent times using refixation or the mechanical reference frame at differing time intervals.  
         [0086]     Variations of the steps shown in  FIG. 19  can be done. For example, steps  1316  and/or  1321  can be eliminated to suit research needs.  
         [0087]     The view of these considerations, as well as appreciated by those skilled in the art, implementation and systems should be considered broadly and with reference to the claims set forth below.