Data for: Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain

Tissue clearing and labeling techniques have revolutionized brain-wide imaging and analysis, yet their application to clinical formalin-fixed paraffin-embedded (FFPE) blocks remains challenging. We introduce HIF-Clear, a novel method for efficiently clearing and labeling centimeter-thick FFPE specimens using elevated temperature and concentrated detergents. HIF-Clear with multi-round immunolabeling reveals neuron circuitry regulating multiple neurotransmitter systems in a whole FFPE mouse brain, and is able to be used as the evaluation of disease treatment efficiency. HIF-Clear also supports expansion microscopy and can be performed on a non-sectioned 15-year-old FFPE specimen, as well as a 3-month formalin-fixed mouse brain. Thus, HIF-Clear represents a feasible approach for researching archived FFPE specimens for future neuroscientific and 3D neuropathological analyses., , , # Data for: **Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain**

[https://doi.org/10.5061/dryad.prr4xgxv7](https://doi.org/10.5061/dryad.prr4xgxv7)

The dataset represents source data used for the figures in our manuscript, \"**Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain**,\" in the journal eLife. Details on the data collection methods are described in our manuscript. For the file naming conventions, the 'Figure1A_SourceData' file includes data necessary for creating Figure 1A of our manuscript. This data contains metrics like fluorescence intensity, cell counts, and morphological assessments of blood vessels and brain structures. Further details on these metrics can be found in the methods section of the manuscript.

Additional resources include the Supplemental information ([https://doi.org/10.5281/zenodo.11100542](https://doi.org/10.5281/zenodo.11100542), which offers a 2-times downsamp...