Standard brain shape model (brain blank map)

Since the size and the shape of the brain, and the positional relationship of the tissues are slightly different for each individual, in order to compare and integrate the  information obtained from different individuals, the difference in size and shape of the brain A standard brain (brain blank map) with an average brain shape corrected and standardized becomes effective.

Step 1

First of all, a confocal continuous image in which the boundary of the brain and the module structure are clearly photographed is taken as the "template image" as a reference. Align each sample brain image with this template image.

Step 2

For the landmark, use the center point of the center body, the center point of the regular glomerule, the center point of the mushroom body umbrella, etc., which is a clearly observable modular structure (neuropile). The standard of positioning is the landmark (reference point) of the external structure of the brain and the tissue structure (module structure etc.) in the brain.

Step 3

Transform (Rigid Transform) for obtaining the average shape of the brain is performed by positioning and size adjustment of the whole brain with reference to these landmarks. By this transformation, the position and angle of the image coordinate point will be changed so that the landmark of the brain image obtained from different individuals will come as close as possible, the brain images of the sample and the template will overlap considerably. Conduct alignment of these two brain images on multiple brain images, and then create an average brain image (Ex01).

  Tutorial movie               Data file: 11_1_1.tgz

Step 4

The average brain image created in the process from step 1 to 3 is separted by a certain threshold level to create a binary cerebral image. Smooth average brain shape image can be obtained by application of 3D smoothing plugin tool of Fiji. By applying the function "Create Surface" provided by the plug-in (IntSeg_3D.jar) , it can be displayed as a three-dimensional image (Ex02). You can also output a average brain shape as a 3D model by using a 3D printer.

Tutorial movie               Data file: 11_1_2.tgz