Notes on Using the Atlas
This atlas is designed as an introduction to human neuroanatomy. Roughly 50 brain regions are labeled (for a list, see here), though many more are visible to the trained eye. If you want to learn about additional brain structures, go to the Human Brain Atlas the Michigan State University Brain Biodiversity Bank.
The Zoomable Human Brain Atlas is based on three normal adult human brains (for more details, see here) that were sectioned either coronally, horizontally, or sagittally (for details on section planes, see here). For each section plane, you can examine either Nissl-stained sections (showing mainly neuronal cell bodies) or adjacent fiber-stained sections (highlighting myelinated axons). Cell groups and ventricles are generally labeled in the Nissl-stained sections, whereas fiber tracts are labeled in the fiber-stained sections (an exception is the globus pallidus, which is easier to see in fiber-stained material). To keep things simple, the atlas includes only about 8-10 sections per stain and section plane, emphasizing sections that include subcortical structures. For additional sections and for details on section location, visit the Human Brain Atlas.
You can view the sections either in “slide show mode” or “menu-driven mode”.
In slide show mode you can see the sections in sequence (e.g., as a slide-show) from anterior to posterior in the coronal plane, from medial to lateral in the sagittal plane, or from superior to inferior in the horizontal plane. An advantage of viewing the sections in this way is that you can easily compare adjacent Nissl-stained and fiber-stained sections, and can rapidly follow large structures across multiple sections. A disadvantage is that in slide show mode none of the structures are labeled. Therefore, it is best to begin your study in the menu-driven mode and then advance to the slide show mode after you already know some key structures. The two modes are complementary. You can also compare adjacent Nissl- and fiber-stained sections in menu-driven mode by opening the relevant series/images in different tabs of your browser and then switching between tabs.
In menu-driven mode you see only one section at a time, but that section is labeled (by default). To see another section in the same series (e.g. coronal sections, Nissl-stained), click on “Display Options” at the top left and go to Image -> Open. You’ll get a scrollable list of available images; these are numbered in sequence. Other useful options in the Display Options menu are “full screen” and “print” (note that the program will adjust the zoom a bit to give you the best print quality; so use print preview before you waste paper; also note that “save file as” is buggy). You also have the option to hide various panels (e.g. the Toolbar) and to show them again (i.e., reset). Zooming in and out of the image, as well as scrolling across it, can be done through the Toolbar. However, you can also use keyboard and mouse controls to zoom and pan (try it and see what works!).
To focus on individual brain regions (see List of Labeled Structures), use the Points-of-Interest (POI) menu at the top left of the window in the menu-driven mode. The structures are listed alphabetically in the pull-down menu. Once you have selected a region of interest, click on the little window in the POI panel to zoom in. As you do this, any relevant notes about the region will appear in the Note panel. These notes are intentionally kept to a minimum and contain no functional information (most structures have multiple functions anyway).
Labels are generally centered on their target structures. In the coronal and horizontal sections structures are labeled on only one side of the brain. Why does the atlas not indicate brain region boundaries? Because for many brain regions drawing their boundaries is actually quite difficult. Many boundaries are fuzzy rather than crisp, and some are discontinuous due to the structure's 3D organization.
However, you can learn to identify many boundaries by looking carefully at the sections. Look at the staining pattern underneath the center of the label (you can toggle the labels on and off by clicking on the diagonal arrow in the Toolbar window) and then examine how far that particular pattern extends. Often this method helps you find key boundaries. Unfortunately, this method is problematic for regions like the dorsal thalamus that comprise many histologically distinct subdivisions (i.e., structures with internal boundaries). In such cases, you'll have to refer to other web sites or textbooks to help you identify what's what. As mentioned earlier, this atlas is intentionally kept simple. Hopefully it will help you learn (at least) the spatial arrangement of the human brain's main components.
If you have suggestions or other comments, please send them to Georg Striedter.