The main object of this project is reconstructs a three-dimensional computerized map of Nissl stained tree shrew brain anatomy with digital imaging processing techniques. The project report described here is the phase one of the 3D tree shrew brain map project. In this phase, the brain of the tree shrew is frozen and cryosectional precision images were digitally captured by digital camera installed on microscope. Due to the limitation of the view field of the microscope and high-resolution requirement for further research of the tree shrew brain visual structure , Each image captured by the digital camera can only cover quarter of the full image of the brain slice. By using phase-correlate alignment algorithm, we can match the four images of each brain slice into one whole tree shrew brain 2D image. 

Specimen Preparation
      The image is based on neuro-anatomic information obtained from an adult male tree shrew. Adult tree shrew was deeply anesthetized with ketamin KCl and followed by lethal dose of beuthanasia delivered intraperitoneally. After perfused transcardially with phosphate buffer, the tree shrew were fixed with 4% paraformaldehyde. After remove the skin and skull of tree shrew, the brain was immersed in 30% sucrose phosphate buffer. After One night, the brain was quickly frozen on dry ice. The frozen brain were sectioned on a cryo-macrotome, and each slice of the brain chip is 40 micron. Brain sections, in which 160 micrometers apart from each other, were stained by Nissl staining. The serial Nissl staining brain slices were fixed in microscope glass. In this project, all we have 36 Nissl staining brain slices. 


Digital Image Acquisition
      Since each slices of brain section of tree shrew is very small. For getting clear and high-resolution images of brain, we magnified the picture of brain slices under AxioVison 2.05 (Zeiss) microscope and captured the images by a digital video camera which were fixed on the microscope. The monochrome video signal was digitized into 1280*1024*8 gray image by a image capture card installed on a IBM-PC compatible computer. Due to the limitation of the view field of the microscope and high-resolution requirement for further research of the tree shrew brain visual structure , Each image captured by the digital camera can only cover quarter of the full image of the brain slice. We take four images for each brain slice, totally, we took 144 images for all those 36 brain slices. 

Enhancement of Image Quality
      Due to the un-uniform of the microscopic illumination and contamination of the microscopic object lens, the acquired images were un-uniformed lighting and have many spots. Below is the reference image and one brain slice image. The reference image was acquired by taking a blank image from the microscope without putting any brain section. 

2D Image Registration 
      By Using Phase-correlate Alignment Algorithm Each image captured by the digital camera can only cover quarter of the full image of the brain slice. For reconstructs a three-dimensional computerized map of Nissl stained tree shrew brain anatomy, we must first match those four images of each brain slice into one whole tree shrew brain 2D image.