The expansion/shrinkage was corrected with furrow initiation, and the cleavage furrow was properly placed (Fig. 3G).
The spliced final 3D reconstruction was corrected for shrinkage in each dimension: x (6.3 %), y (6.0 %) and z (8 %) (Sadek et al. 2007).
When advisable due to high dimensionality of features, the estimation of the covariance matrix that is needed for LDA was corrected by shrinkage (Ledoit and Wolf 2004; Vidaurre et al. 2009).
To compare the results of volume estimates with other reports, the volume was corrected for 47% tissue shrinkage during dehydration for the autism group and 45% shrinkage for the control group.
P-values were adjusted using an empirical Bayes shrinkage of standard error, and false discovery rate was corrected using the method of Benjamini and Hochberg [54].
The shrinkage that occurs in the z-axis of the brain sections during dehydration was corrected with the software.
Different staining procedures could lead to slight differences in tissue shrinkage (that has not been corrected here).
Thirdly, tissue shrinkage was not corrected and since the atlas is made from free-floating sections, there is a slight decrease in accuracy when moving far away from the midline.
The scale bars in the figures are corrected for shrinkage caused by ISH.
All volumes and thicknesses were corrected for shrinkage, as assessed by comparing the diameter of maternal erythrocytes on slides with diameter measurements obtained from fresh maternal erythrocytes, as previously described (14).
Therefore, the total numbers of neurons in the whole column and in the cortical layers did not have to be corrected for shrinkage due to fixation and embedding artifacts.
