Light-sheet fluorescence microscopy images of optically cleared and c-Fos immunolabeled mouse brain

Provided dataset constitutes a part of a tutorial for the LSFMPy software package. It comprises two image stacks of an optically cleared mouse brain hemisphere acquired with a light-sheet fluorescence microscope. The two stacks correspond to two channels, imaged at different excitation wavelengths: 488 nm (autofluorescence) and 638 nm (c-Fos immunolabeling). The tutorial guides the user through the process of converting image dataset to hdf5-based data format, affine coregistration of the two channels, alignment to the Allen Mouse Common Coordinate Framework v3 (CCF v3), and using LSFMPy to leverage obtained transformations to map image data between spaces in a variety of applications. A broader description of the data, the software package and the study can be found in the related publication.