Overlap Between Sections in Developing Mouse Brain Atlas

The developing mouse brain atlas documentation says that the brain slices were cut at 20 µm thickness. The documentation also says that there were multiple animals used to create this atlas. My questions is, is there any overlap between one section to another? If so, if I were to take a range of images, how thick should I consider the tissue in that image range to be? Ex. 10 images would, according to the 20 µm thickness, be 200 µm total. But if there is overlap it could be anywhere between 10 µm - 200 µm thickness.

Thanks for your question!

There wasn’t any overlap between sections in the developing mouse brain atlas, so users should assume the range/thickness of tissue is (# of images x sectioning thickness). Sectioning thickness was 20um for E11.5 > P4 and 25um for P14 and P28.

Thank you for your reply. However, it does not make logical sense to me. Firstly, 498 images at 25 µm results in a brain that is 12.45 mm long, which is larger that the 12 mm the adult mouse brain atlas shows. Secondly, the reason given for not having bregmas in the developing mouse brain atlas is that multiple animals were used, each with their own individual bremga point, and, as a result, no true bregma identifiers can be placed on the tissue. If each animal has their own individual bregma, and tissue from multiple animals was used, this suggests that the images are not strictly sequential to each other. Which, in turn, suggests that each image has some overlap with either or both of the images on either side of it. The reason this is something I am trying to determine is that I am trying to work out how many images would constitute the equivalent of a 40 µm thick section.

Hi, are you referring to gene expression ISH data or the reference atlases specifically?

The reference atlases.