DOI: 10.5061/dryad.prr4xgxv7
title: Data for: Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain

description: 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.
description: # 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 downsampled isotropic image dataset of Tyrosine hydroxylase (TH) immunolabeling shown in Figure 4. ## Description of the data and file structure **Figure 1A:** Comparison of DiD signal intensity across different treatments in 2-mm-thick slices of mouse brain. * **Figure1A_SourceData:** Includes ROI ID, area in pixels, and summed DiD fluorescence intensities for each treatment. **Figure 1F:** Statistical analysis of the gray values in brains processed with different methods. * **Figure1F_SourceData:** Includes ROI ID and summed gray values under three different processing conditions. **Figure 2B:** Comparison of brain region volumes between the hemispheres in a treated mouse brain. * **Figure2B_SourceData:** Lists full names and acronyms of brain regions, along with volumes in cubic millimeters for left, right, and total brain regions. **Figure 7F:** Quantification of astrocytes categorized by distance from the tumor surface. * **Figure7F_SourceData:** Includes classification IDs, distance ranges, and counts of astrocytes. **Figure 7K:** Evaluates the therapeutic effects of different treatments using three indicators. * **Figure7K_SourceData:** Features the indicators and the comparative therapeutic effects across treatment and sample preparation pairs. **Figure 7M:** Measures various aspects of blood vessel morphology. * **Figure7M_SourceData:** Contains four tabs with data on area, volume, length, and bifurcations in both micrometers and pixels. **Figure 7—figure supplement 2:** Shows identical statistical trends between two sample preparation methods. * **Figure7Supplement_SourceData:** Includes various tabs for therapeutic effect indicators and detailed metrics for three replications of each group. **Figure 8C:** Profiles of axon signal intensity. * **Figure8C_SourceData:** Provides gray values along specified Y-positions marked in the figures. This dataset aims to facilitate replication of our results and encourage further exploration using the provided data.