Introduction

Here, we introduce the procedures for creating a standard brain as an example of silkworms, and explain how to segment and register (register) the neuropile and neurons into the standard brain.

What is the standard brain?

The standard brain is a brain image and a map showing the average shape and positional relation. For the silkworm brain, it was created by obtaining the average brain shape from the brain image obtained by the confocal laser microscope and registering the brain tissue image with this. This image can be used for extraction and registration of neuropile and tract and so on.

　In addition to the main program, please install the following plug-in.

・plugin for load and save NIfTI formatted image file (nifti_io.jar)

・Separation of background and objects by maximum entropy method (Entropy_Threshold.class)

・Registration of neuron morphology data by Thin-plate spline transformation (NeuroRegister_.jar)

・Construction of morphological model from extracted neuropile and neuron (IntSeg_3D.jar)

2) Segmentation software　ITK-SNAP

3) Neuron segmentation software　SIGEN 　KNEWRiTE