Brain Maps Atlases

A. AN OPEN ACCESS ATLAS
B. BRAIN MAPS 3 (2004): Overview of the artwork files
C. ATLAS LEVELS (ALs): Download Adobe Illustrator files
D. TEXT OF BRAIN MAPS, 3rd EDITION (2004)

 
A. AN OPEN ACCESS ATLAS:
 
BM3 Front coverFront cover of Brain Maps, third edition (2004)

 

The first three editions of Brain maps: structure of the rat brain were published by Elsevier (see Books), and in 2013 the publisher returned all legal rights associated with the contents to Larry—including also rights to the companion Developmental brain maps: structure of the embryonic rat brain (1996).

On this page, the third edition of Brain maps (BM3) is provided for viewing and download. Atlas Levels for the first two editions of Brain Maps are provided for download on the Brain Maps 1 and Brain Maps 2 pages, and the complete Developmental brain maps is supplied on the Developmental Brain Maps page. Beta (Preview) versions of parts of the open access Brain maps 4.0 will be posted on the BM4 beta page as they are completed.

Anyone is free to use the materials in these books, with the Atlas Levels being especially useful for illustrating the location of features as seen in cross sections (transverse levels through the brain). This material is now open access and simply licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Adobe Illustrator files for all Atlas Levels are available below.

 

B. BRAIN MAPS 3 (2004): Overview of the artwork files

To get an overview of the 73 Atlas Levels (Mapping only version), scroll through the open access pdf app for your laptop, iPad, or smartphone (many thanks to Arshad Khan and Ellen Walker, UTEP, for putting it together). “Map only Atlas Levels” are simple drawings for mapping results.

Open the pdf files in Adobe Illustrator for editing the drawings and adding data layers over the maps. Here’s a sample. Insert the pdf files in PowerPoint for simple resizing, cropping, and additional labeling. You are free to use the figures as long as you adhere to terms of the Creative Commons Attribution-NonCommercial 4.0 International License—basically no commercial use and cite the source, Swanson, L.W. (2004) Brain maps: structure of the rat brain, 3rd edition.

In the “Complete Atlas Level” files, illustrations are arranged in 9 layers that can be viewed in any combination:
(be sure to view Window Layers Screen in Adobe Illustrator)

Top layer (1): “new art” for users to add data over the map template below.
Next layer (2): “stereotaxic coordinates” for structures in the Atlas Level, corrected to correspond to Paxinos & Watson (1986).
Next layer (3): “Nissl” is a screen resolution image of the cell-stained histological section for the map; low resolution but useful for orientation.
Next layer (4): “abbreviation list” for parts labeled in the map.
Next layer (5): “box for database/3D model” for keep sequential Atlas Levels in register (see NeuART-II).
Next layer (6): “atlas” map for the Atlas Level.
Next layer (7): “subdivision color coding” for the major parts of the brain shown on the flatmap and in the nomenclature tables.
Next layer (8): “yellow mask” is a simple opaque background for the map.
Bottom Layer (9): “physical coordinates” are the actual dimensions of the brain after histological processing.

 

C. ATLAS LEVELS (ALs):Download Adobe Illustrator files
Atlas levels (sagittal) BM3Atlas Levels in Swanson, L.W. (2004) Brain maps, 3rd edition

“Map only Atlas Levels” are simple drawings for mapping results.

Complete Atlas Level 01
Map only Atlas Level 01

Complete Atlas Level 02
Map only Atlas Level 02

Complete Atlas Level 03
Map only Atlas Level 03

Complete Atlas Level 04
Map only Atlas Level 04

Complete Atlas Level 05
Map only Atlas Level 05

Complete Atlas Level 06
Map only Atlas Level 06

Complete Atlas Level 07
Map only Atlas Level 07

Complete Atlas Level 08
Map only Atlas Level 08

Complete Atlas Level 09
Map only Atlas Level 09

Complete Atlas Level 10
Map only Atlas Level 10

Complete Atlas Level 11
Map only Atlas Level 11

Complete Atlas Level 12
Map only Atlas Level 12

Complete Atlas Level 13
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Complete Atlas Level 14
Map only Atlas Level 14

Complete Atlas Level 15
Map only Atlas Level 15

Complete Atlas Level 16
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Complete Atlas Level 17
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Complete Atlas Level 18
Map only Atlas Level 18

Complete Atlas Level 19
Map only Atlas Level 19

Complete Atlas Level 20
Map only Atlas Level 20

Complete Atlas Level 21
Map only Atlas Level 21

Complete Atlas Level 22
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Complete Atlas Level 23
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Complete Atlas Level 24
Map only Atlas Level 24

Complete Atlas Level 25
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Complete Atlas Level 26
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Complete Atlas Level 27
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Complete Atlas Level 28
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Complete Atlas Level 29
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Complete Atlas Level 30
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Complete Atlas Level 31
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Complete Atlas Level 32
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Complete Atlas Level 33
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Complete Atlas Level 34
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Complete Atlas Level 35
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Complete Atlas Level 36
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Complete Atlas Level 37
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Complete Atlas Level 38
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Complete Atlas Level 39
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Complete Atlas Level 40
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Complete Atlas Level 41
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Complete Atlas Level 42
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Complete Atlas Level 43
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Complete Atlas Level 44
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Complete Atlas Level 45
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Complete Atlas Level 46
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Complete Atlas Level 47
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Complete Atlas Level 48
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Complete Atlas Level 49
Map only Atlas Level 49

Complete Atlas Level 50
Map only Atlas Level 50

Complete Atlas Level 51
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Complete Atlas Level 52
Map only Atlas Level 52

Complete Atlas Level 53
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Complete Atlas Level 54
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Complete Atlas Level 55
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Complete Atlas Level 56
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Complete Atlas Level 57
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Complete Atlas Level 58
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Complete Atlas Level 59
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Complete Atlas Level 60
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Complete Atlas Level 61
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Complete Atlas Level 62
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Complete Atlas Level 63
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Complete Atlas Level 64
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Complete Atlas Level 65
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Complete Atlas Level 66
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Complete Atlas Level 67
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Complete Atlas Level 68
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Complete Atlas Level 69
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Complete Atlas Level 70
Map only Atlas Level 70

Complete Atlas Level 71
Map only Atlas Level 71

Complete Atlas Level 72
Map only Atlas Level 72

Complete Atlas Level 73
Map only Atlas Level 73

 

D. TEXT OF BRAIN MAPS, 3rd EDITION (2004) (oversize format; leaves 43.3×28.0 cm, spiral bound)
Abbreviations, BrainMaps3 (2004) (view pdf); Abbreviations, BrainMaps3 (2004) (download .doc)

 

BM3 Frontispiece: Flatmap with all white matter tracts

BM3 Title-page

BM3 Imprint

 

1, Introductory, BrainMaps3 (2004): Preface, Table of contents, Overview, Summary of rat brain structure

2, Atlas prep, BrainMaps3 (2004): Histology & map production, Coordinate systems, Changes since 2nd edition

3, Mapping, BrainMaps3 (2004): Neuroanatomical methods, Transferring data to atlas, Databases, 3D models

4, Flatmaps, BrainMaps3 (2004): Overview

4a, BM3 rat flatmap 3.0 foldout poster

5, Nomenclature, BrainMaps3 (2004): Discussion of some major problems

6, Atlas guide, BrainMaps3 (2004): Overview of the 73 transverse levels

7, References, BrainMaps3 (2004)

 

8, Nomenclature tables BM3: Appendix (overview of Annotated Nomenclature Tables A-D)

8a, Table A, BM3: Annotated Nomenclature Table A, Major parts of the mammalian nervous system

8b, Table B, BM3: Annotated Nomenclature Table B, Basic cell groups or regions of the rat central nervous system

8c, Table C, BM3: Annotated Nomenclature Table C, Basic fiber systems or white matter tracts of the rat central nervous system

8d, Table D, BM3: Annotated Nomenclature Table D, Gross anatomical features of the rat peripheral nervous system

 

9, Index, BrainMaps3 (2004)

 

10, CD User guide, BrainMaps3(2004): Tips on using the downloadable Interactive brain maps Adobe Illustrator files. They are part of the complete set of files on the CD-ROM, Computer graphics files 3.0.

 

10a, Atlas Levels on rat flatmap: Contours of cerebral cortical areas from Atlas Levels plotted on the flatmap

10b, Rat hippocampus flatmap 2.0: Version 2.0 of contours of hippocampal region areas from Atlas Levels plotted on a flatmap

10c, Human flatmap 1.0

10d, Determine section angle: Determine cutting angle of histological sections from internal fiducials (see User Guide)

10e, Interbrain section angle: Determine cutting angle of histological sections for interbrain specifically (see User Guide)

10f, Sample database (AL19): An Atlas Level with multiple overlaying data layers, prototype of NeuARt application (see User Guide)

10g, Sample database layer for 10f: Example of a single data layer for the atlas database (10f)

 

ERRATA for third edition:

 
BM3 Back coverBack cover of Brain Maps, third edition (2004) L.W. Swanson