Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

Arshad M Khan et al. Front Syst Neurosci. 2018.

Abstract

The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that _z_-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including neuronal cell bodies, axons, and chemoarchitecture; to generate data-constrained hypotheses difficult to formulate otherwise. The alignment strategies provided in this study constitute a basic starting point for first-order, user-guided data migration between PW and S reference spaces along three dimensions that is potentially extensible to other spatial reference systems for the rat brain.

Keywords: atlas; behavioral control; computer vision; data migration; registration; stereotactic; stereotaxic; subject matter expert.

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Figures

Figure 1

Pseudocode delineating the operations of the custom-made algorithm developed for this study, based on SIFT and RANSAC operations.

Figure 2

Cleveland dot plot charts illustrating craniometric alignments of sequential levels for Paxinos & Watson (PW) reference atlases with the Swanson (S) reference atlas. The charts are calibrated to a millimeter scale (found at the top of A,B) denoting anteroposterior (AP) distance from the cranial suture-based landmark, Bregma (β). The legend at the bottom of the figure defines each symbol, with filled black dots, filled red dots, and open circles in PW spaces denoting levels that are fully in register, not in register, or narrowly in register; respectively, with the corresponding dots directly below them in S space. (A) Cleveland plots aligning the atlas levels of two PW reference spaces (“PW1 Levels” and “PW2 Levels”) to S reference space (“S Levels”). “PW1 Levels” denote atlas levels from the first three editions of The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (1982, 1986, 1997) and are designated “PW82,” “PW86,” and “PW97,” respectively. “PW2 Levels” denote atlas levels from the fourth edition of The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (1998), which is designated “PW98.” Editions 2–4 contain refinements of the atlas drawings in the first edition, but the actual tissue sections on which the drawings are based are the same as those used in the original edition. *The only exception to this rule is that “PW98.” differs from “PW82,” “PW86,” and “PW97_” in the addition of two levels from the original tissue set that had not been published in the earlier editions. These are highlighted as filled blue dots. Because these additions alter the numbering scheme for the “_PW98_” levels from those of previous PW editions, they have been displayed separately from those editions. (B) Cleveland plots aligning the atlas levels of a third PW reference space (“_PW3 Levels”) to S reference space (“S Levels”). “PW3 Levels” denote atlas levels from the fifth, sixth and seventh editions of The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005, 2007, 2014) and are designated “PW05,” “PW07,” and “PW14,” respectively. They are in a separate reference space because the tissue used was from a different animal than that used for the earlier editions, which were actually based on tissue sections from several animals. (A,B) “S Levels_” comprise atlas levels from all four editions of Brain Maps: The Structure of the Rat Brain by Larry W. Swanson, published in 1992, 1998, 2004, and 2018 (designated “_S92,” “S98,” “S04,” and “_S18_”; respectively). They are all within one reference space because the same tissue set has been used for each edition, with the editions differing primarily in the refinement of the drawings and cytoarchitecturally derived mapped sub-regions from this single tissue set.

Figure 3

Points of interest found in a region of interest from a plate in the (A) Paxinos and Watson (2014) atlas and (B) in the Swanson (2004) atlas. The small horizontal lines in each panel inside the circular regions indicate the region's dominant orientation. Different region sizes correspond to different scales. The portion of the PW14 atlas photomicrograph (Level 70) is reproduced in (A) with permission from Elsevier. The photomicrograph in (B) is reproduced from Swanson (2004) under the conditions set forth by a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

Figure 4

Results of Experiment 1a. The algorithm successfully matched the exact S atlas plate (Level 34), containing the desired Nissl-stained tissue section, with the ROI extracted digitally from that section, which was rotated 155 degrees and distorted slightly through random point-warping, and used as a test image. SIFT matches are shown for the test image before (A) and after (B) RANSAC was applied to remove outliers. The photomicrographs are reproduced from Swanson (2004) under the conditions set forth by a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/ 4.0/legalcode

Figure 5

Results of Experiment 1b. Examples of a good match between an ROI and an image (A), and a poor one (B). The photomicrographs are reproduced from Swanson (2004) under the conditions set forth by a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

Figure 6

Results of Experiment 2. View of the match obtained after Experiment 2 was implemented, between an ROI extracted from PW space and the closest matching S atlas photomicrograph. In the inset (labeled A), the portion of the PW14 atlas photomicrograph (Level 70) is reproduced with permission from Elsevier. The photomicrograph in the main image is reproduced from Swanson (2004) under the conditions set forth by a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

Figure 7

Summary of Experiment 2. The algorithm successfully matched its top-ranked S atlas plates (most plates within Levels 29–36) with the ROI extracted digitally from Plate 70 of PW3 space. This range is in close agreement with the general range of levels between the two reference spaces, as indicated by craniometric measures.

Figure 8

(A) A representative example of a microinjection site, with the injection scar denoted by a white asterisk (*). This photomicrograph shows one half of a transverse section through the rat brain, with a needle track targeting the hypothalamus. o, optic tract. Scale bar = 1 mm. (B) Sequential steps in the transformation of a graphical injection site drawing to a vector-formatted object: Step 1: graphical drawing based on _PW_86; Step 2: the _PW_98 digital version of the same atlas drawing; Step 3: an overlay of the drawing in 1 and the digital drawing in 2 (graphical drawing over digital boundaries); Step 4: vector drawing, in a separate layer, of the injection site. The portion of the PW atlas figure (Level 26) is reproduced here with permission from Elsevier.

Figure 9

Point-source data migrated from the digital map in Paxinos and Watson (1998), Figure 26, to Swanson (2018), Level 26. (A) Paxinos and Watson (1998), Figure 26. Point-source data are shown by red dots, which have been shifted contralaterally. (B) Swanson (2018), Level 26, with stereotaxic grid aligned to that of Paxinos and Watson (1998), Figure 26. Point-source data appear at their original stereotaxic coordinates. (C) Swanson (2018), Level 26, with stereotaxic grid aligned to that of Paxinos and Watson (1998), Figure 26. Point-source data have been shifted to more closely match their original locations with regard to nearby fiducials. Note that to minimize reader distraction, the general appearance (but not boundaries or nomenclature) of the S levels in (B,C) have been altered to match those of PW. Figure 26 from PW98 is reproduced with permission from Elsevier. Level 26 from S18 is reproduced from Swanson (2018) under the conditions of a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

). For an explanation of the abbreviations in A, see List of Abbreviations, Paxinos and Watson Nomenclature. For an explanation of the abbreviations in B and C, please see List of Abbreviations, Swanson Nomenclature.

Figure 10

Point-source data migrated from Paxinos and Watson (1998), Figure 31, to Swanson (2018), Level 29. (A) Paxinos and Watson (1998), Figure 31. Point-source data are shown by red dots, which have been shifted contralaterally; and blue dots, which have not been shifted. (B) Swanson (2018), Level 29, with stereotaxic grid aligned to that of Paxinos and Watson (1998), Figure 31. Point-source data appear at their original stereotaxic coordinates. (C) Swanson (2018), Level 29, with stereotaxic grid aligned to that of Paxinos and Watson (1998), Figure 31. Point-source data have been shifted to more closely match their original locations with regard to nearby fiducials. Note that to minimize reader distraction, the general appearance (but not boundaries or nomenclature) of the S levels in (B,C) have been altered to match those of PW. Figure 31 from PW98 is reproduced with permission from Elsevier. Level 29 from S18 is reproduced from Swanson (2018) under the conditions of a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

Figure 11

Point-source data migrated from Paxinos and Watson (1998), Figure 33, to Swanson (2018), Level 30. (A) Paxinos and Watson (1998), Figure 33. Point-source data are shown by blue dots. (B) Swanson (2018), Level 30, with stereotaxic grid aligned to that of Paxinos and Watson (1998), Figure 33. Point source information appears at its original stereotaxic coordinates. (C) Swanson (2018), Level 30, with stereotaxic grid aligned to that of Paxinos and Watson (1998), Figure 33. Point source data have been shifted to more closely match their original locations with regard to nearby fiducials. Note that to minimize reader distraction, the general appearance (but not boundaries or nomenclature) of the S levels in (B,C) have been altered to match those of PW. Figure 33 from PW98 is reproduced with permission from Elsevier. Level 30 from S18 is reproduced from Swanson (2018) under the conditions of a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

Figure 12

Summary of migration analysis conducted by converting each S atlas reference quadrant into a Cartesian plane. Scales on the ordinate and abscissa are in millimeter units. Each row shows the migration from a different source PW level to its corresponding (most closely matching) level in S space: _PW_9826 formula image _S_26 (top row), _PW_9831_S_29 (middle row), and _PW_9833_S_30 (bottom row). The columns show the position of the migrated points in S space before (left column) and after (middle column) expert-guided mapping adjustments and corrections were made. Right column: the vectors for each pair of original and relocated points are shown within a unit circle with origin m (to denote the medial-most point), mediolateral _x_-axis (l, lateral), and dorsoventral _y_-axis (d, dorsal; v, ventral). Point-source data are shown by red dots, which have been shifted contralaterally; and blue dots, which have not been shifted.

Figure 13

Migrated data coded by behavioral experiment. The injection cases involving Experiment 4 of Khan et al. (2004) are shown in their final migrated states. In (A), the injection sites migrated from Paxinos and Watson (1986) (PW86), Level 31, are shown in their host reference space [(Swanson, 2018) (S18); Level 29]. In (B) the injection sites migrated from PW86, Level 33, are shown in S18, Level 30. The scales flanking these panels mark the estimated stereotaxic coordinates in the mediolateral (x) and dorsoventral (y) dimensions, derived from PW86 and encoded within S18. The _x_-axis scale applies to both (A,B). Note that expert-guided intervention was required to make adjustments of the injection sites to their final locations, and thus the plotted points should be considered as first-order approximations of the actual injection sites. The letters denoting each site refer to case numbers, which are found for the corresponding levels in Table 7 for the “_PW_31 formula image _S_29” migration (A) and “_PW_33_S_30” (B). (C) Structures of the reagents injected: the protein tyrosine kinase inhibitor, Tyrphostin A48 (A48), and the glutamate receptor agonist, _N_-methyl-

-aspartate (NMDA). (D) The behavioral results, adapted from Khan et al. (2004), associated with the injection sites mapped in A and B. Two injections were delivered to each site, 10 min apart, with A48 injected before NMDA. All injection volumes were 300 nl, containing the doses of the reagents as indicated. The asterisk marks significant overall cumulative food intake triggered by NMDA injection relative to vehicle injection, and the inverted carat denotes significant suppression of NMDA-elicited eating at the highest dose of A48 tested (P < 0.5). See Khan et al. (2004) for details. Permission to reproduce the data in D from Khan et al. (2004) has been provided under the permissions policy of The Journal of Neuroscience. Levels 29 and 30 from S18 are reproduced from Swanson (2018) under the conditions of a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

). For an explanation of the abbreviations on this figure, please see the List of Abbreviations, Swanson Nomenclature.

Figure 14

Migrated data coded by behavioral experiment. The injection cases involving Experiment 5a and Experiment 5b of Khan et al. (2004) are shown in their final migrated states. In (A), the injection sites for Experiment 5a, migrated from Paxinos and Watson (1986) (PW86), Level 31, are shown in their host reference space (Swanson, (S18); Level 29). In (B), the behavioral data, adapted from Khan et al. (2004), are shown that are associated with the injection sites in (A), along with the chemical structure of the protein tyrosine kinase inhibitor, PP1. Two injections were delivered to each site, 10 min apart, with PP1 injected before NMDA. All injection volumes were 300 nl, containing the doses of the reagents as indicated. The asterisk denotes significantly greater cumulative food intake overall relative to vehicle controls, and the inverted carats denote significant suppression of cumulative food intake relative to NMDA-elicited eating (P < 0.5). See Khan et al. (2004) for details. In (C,D), the injection sites for _Experiment 5b_—and for an associated experiment not reported in Khan et al. (2004) (see cases marked with an asterisk in Table 7)—migrated from PW86, Level 26 and 31; are shown in S18, Level 26 and 29, respectively. Associated behavioral results for this experiment are not shown here, but can be found in the descriptive narrative of the Results section in Khan et al. (2004). The scales flanking these panels mark the estimated stereotaxic coordinates in the mediolateral (x) and dorsoventral (y) dimensions, derived from PW86 and encoded within S18. The _x_-axis scale in (A) applies to both (A,B). Note that expert-guided intervention was required to make adjustments of the injection sites to their final locations, and thus the plotted points should be considered as first-order approximations of the actual injection sites. The letters denoting each site refer to case numbers, which are found for the corresponding levels in Table 7 for the “_PW_31 formula image _S_29” migration (A) and “_PW_26_S_26” and “_PW_31_S_29” migrations (C,D). Permission to reproduce the data in B from Khan et al. (2004) has been provided under the permissions policy of The Journal of Neuroscience. Levels 26 and 29 from S18 are reproduced from Swanson (2018) under the conditions of a Creative Commons BY-NC 4.0 license (

https://creativecommons.org/licenses/by-nc/4.0/legalcode

). For an explanation of the abbreviations on this figure, please see the List of Abbreviations, Swanson Nomenclature.

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References

1. Allen G. V., Cechetto D. F. (1993). Functional and anatomical organization of cardiovascular pressor and depressor sites in the lateral hypothalamic area. II. Ascending projections. J. Comp. Neurol. 330, 421–438. 10.1002/cne.903300310 - DOI - PubMed
1. Andreas A., Legler R. (1969). Ein Gerät für stereotaktische Hirnoperationen an der Ratte. Acta Biol. Med. Germ. 23, 621–625. - PubMed
1. Asimov I. (1942). Foundation. Astound. Sci. Fiction 29, 38–52.
1. Beattie J. (1952). A stereotaxic instrument for placing lesions in the brain of the albino rat. Q. J. Exp. Physiol. Cogn. Med. Sci. 37, 224–232. 10.1113/expphysiol.1952.sp000998 - DOI - PubMed
1. Blasiak T., Czubak W., Ignaciak A., Lewandowski M. H. (2010). A new approach to detection of the Bregma point on the rat skull. J. Neurosci. Methods 185, 199–203. 10.1016/j.jneumeth.2009.09.022 - DOI - PubMed

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