Lin, Ya-HuiYa-HuiLinWang, Li-WenLi-WenWangChen, Yen-HuiYen-HuiChenChan, Yi-ChiehYi-ChiehChanHu, Shang-HsiuShang-HsiuHuWu, Sheng-YanSheng-YanWuChiang, Chi-ShiunChi-ShiunChiangHuang, Guan-JieGuan-JieHuangYang, Shang-DaShang-DaYangChu, Shi-WeiShi-WeiChuKUO-CHUAN WANGLin, Chin-HsienChin-HsienLinPEI-HSIN HUANGCheng, Hwai-JongHwai-JongChengChen, Bi-ChangBi-ChangChenChu, Li-AnLi-AnChu2024-11-192024-11-192024-05-22https://scholars.lib.ntu.edu.tw/handle/123456789/723140Tissue-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.entrueFFPEarchived tissueshumanmousemultiplexed stainingneurosciencetissue clearingwhole brain analysiswhole mouse brain imagingjournal article10.7554/eLife.93212387751332-s2.0-85194018762