Table 3

List of the seven default coordinates used in the “choice game” to align experimental whole-brain mouse LSFM images to the Allen Mouse Brain Atlas (AMBA)

AP
coordinate
Plate
#
Anatomical landmarks and characteristics
+1.9135(1) The folds separating the piriform area (PIR) from the orbital area (ORB) span across approximately half the horizontal length of a hemisphere.
(2) There is a distinct teardrop shape to the anterior commissure, olfactory limb (aco).
(3) The nucleus accumbens (ACB) has not yet appeared.
+1.1043(1) The two “wings” of the corpus callosum, anterior forceps (fa) are just about to touch.
(2) The diagonal band nucleus (NDB) is clearly present and extends halfway the length from the ventral-most point of the midline to the corpus callosum.
−0.4258(1) The columns of the fornix (fx) and the stria medullaris (sm) have just separated; the stria medullaris is still connected in one piece.
(2) The optic chiasm (och) is directly below the hypothalamus in one piece and has not yet split into two optic tracts (opt).
−0.9363(1) The CA3 stratum oriens (CA3so) of the hippocampus is just beginning to show within the fimbria (fi); however, multiple layers of the CA3 are not showing yet.
(2) The columns of the fornix (fx) have migrated below the top of the third ventricle.
(3) The optic tracts have migrated close to the border of the hypothalamus and amygdala.
−1.9473(1) The dentate gyrus (DG) is clearly present and spans approximately 2/3 the horizontal length of one wing of the hippocampus.
(2) The ventral-most point of the granule layer of the dentate gyrus (DG-sg) is roughly the same height as the ventral-most point of the pyramidal layer of CA3 (CA3sp).
(3) The fasciculus retroflexus (fr), mammillothalamic tract (mtt), and columns of the fornix (fx) are clearly seen in their appropriate positions and spaced evenly apart; the mtt is slightly closer to the fx than the fr.
(4) The median eminence is (ME) is clearly visible at the bottom of the midline.
−2.9583(1) The medial mamillary nucleus (MM) of the hypothalamus has receded and is connected by a thinned layer of hypothalamic tissue.
(2) the posterior commissure (pc) and cerebral aqueduct have migrated down from the 3rd ventricle (V3), and they are separated from V3 by sublayers c and b (SCig-c, S-Cig-b) of the superior colliculus.
−3.9693(1) The tegmental reticular nucleus (TRN) and pontine gray (PG) are easily identified and separated by the corticospinal tract (cst) and medial lemniscus (ml).
(2) The brachium of the inferior colliculus (bic) protrudes out to the left and right of the midbrain, slightly beyond the middle cerebral peduncle (mcp).
  • Detailed descriptions of the anatomic landmarks used to match experimental images with the plates are listed. Region acronyms used in the AMBA are also provided so users can cross validate with the AMBA (http://atlas.brain-map.org/atlas?atlas=1).