Planes
Coronal sections run from ear to ear, sagittal sections from front to back down the midline, and transverse (horizontal or axial) sections across the long axis. In the fly brain the coronal view is called frontal.
Brain and spinal cord sections
Ten reference atlases of the brain and spinal cord of six species commonly used in neuroscience, shown in a single viewer. Every region in each of the 363 sections is labelled.
Organism
Atlas
Sections
Zoom with the buttons, by double-clicking or with Ctrl and the scroll wheel; drag to move a zoomed image.
Regions in this section
Section planes and orientation
Directions
Dorsal is towards the back or top, ventral towards the belly or bottom; rostral or anterior is towards the nose, caudal or posterior towards the tail. Each viewer labels its edges.
Templates and histology
MRI templates average many brains, so they show typical shape but not cells. Histology, such as Nissl staining, shows the cells of a single specimen. Each atlas states which method it uses.
Coordinates
Positions are given in each atlas’s own system, for example MNI coordinates for the human brain, Waxholm space coordinates in the rat or distance from bregma in the mouse. They are not interchangeable between atlases.
Atlases in the library
| Atlas | Method | Resolution | Sections | |
|---|---|---|---|---|
| Human Brain | In vivo MRI (T1-weighted population-average template) with anatomical labels registered from Mindboggle-101 and manually corrected | 1 mm isotropic (shown at native resolution) | Coronal 40 sections · 51 regions | Open · Source |
| Human Brain histology | Cell-body (Merker) stained histology, 7,404 coronal 20 µm sections reconstructed in 3D | Images from the 100 µm isotropic volume (shown at 133 µm/px, linear contrast stretch); tissue classes from the 200 µm classified volume, shown at 400 µm | Coronal 40 sections · 9 regions | Open · Source |
| Human Spinal cord | MRI template of 50 adults with a probabilistic grey and white matter tract atlas | 0.5 mm | Transverse 26 sections · 21 regions | Open · Source |
| Mouse Brain | Reference atlas built from serial two-photon tomography of many mouse brains | 10 µm volume; outlines drawn from it | Coronal 29 sections · 382 regions | Open · Source |
| Mouse Developing brain | Histology: whole-embryo sections stained with Feulgen-HP yellow (E11.5–E15.5) and Nissl-stained brain sections (E18.5–P56), with expert manual annotation polygons | Sagittal sections 20 µm thick (E11.5–P4) or 25 µm (P14, P56); images downsampled to 1000 px on the long side (about 6–16 µm per pixel depending on age) | Sagittal 42 sections · 1575 regions | Open · Source |
| Mouse Spinal cord | Nissl histology with atlas drawings by Charles Watson and Gulgun Sengul | About 1 µm per pixel in the original scans | Transverse 34 sections · 88 regions | Open · Source |
| Rat Brain | Ex vivo MRI (T2*-weighted) and diffusion tensor imaging | 39 µm isotropic (labels resampled to 49 µm for display) | Coronal 40 sections · 224 regions | Open · Source |
| Marmoset Brain | Ex vivo MRI (T2-weighted population average) with atlas region segmentation | 100 µm isotropic (labels shown at native resolution; template upsampled 3× for display) | Coronal 40 sections · 250 regions | Open · Source |
| Zebrafish Larval brain | Confocal microscopy of live transgenic larvae registered to a common reference (Zebrafish Brain Browser, ZBB); regions segmented from registered transgene expression patterns | Reference brain 1 µm isotropic (vglut2a reporter, ZBB); region atlas 2 µm isotropic; labels shown at 2 µm, images at 1 µm | Transverse 36 sections · 107 regions | Open · Source |
| Fruit fly Brain | Confocal microscopy; groupwise-registered, left-right symmetric average template (124 images including left-right flips) | Template as distributed by VFB: 0.519 × 0.519 × 1 µm; labels downsampled to 2.08 µm per pixel for display; each level is a single 1 µm section, about 4.4 µm apart | Frontal 36 sections · 46 regions | Open · Source |
Reuse of these atlases is governed by each provider’s terms; most permit non-commercial educational use with citation.
Last updated