A novel method for three‐dimensional observation of the vascular networks in the whole mouse brain

A novel method for acquiring serial images suitable for three‐dimensional reconstruction of vascular networks in the whole brain of mouse was developed. The brain infused with a White India ink‐gelatin solution was fixed and embedded in paraffin containing Sudan Black B through xylene also containing Sudan Black B. Each sliced surface of the paraffin block was coated with liquid paraffin and its image was serially acquired. Coating with liquid paraffin extremely improved the quality of the image. The series of serial images was free of distortion and a three‐dimensional image was reconstructed without the problem of the alignment and registration of adjacent images. The volume‐rendered image indicated three‐dimensional distribution of blood vessels in a whole brain. No ghost or shadow was observed on a volume‐rendered image of the White India ink‐gelatin infused brain. The z‐axial resolution examined on the orthogonal sections reconstituted from serial images obtained at an interval of 5 μm showed no cross talk, indicating that the z‐axial resolution was no larger than 5 μm. A proper understanding of the vascular system in a whole brain is indispensable to reveal the development of the vascular system in the brain of normal and genetically manipulated mouse and vascular alterations in pathological situation, such as stroke and neurodegenerative disease. Although simple and inexpensive, this method will provide fundamental information on the vascular system in a whole brain. Microsc. Res. Tech., 2008. © 2007 Wiley‐Liss, Inc.