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Standard brain of silkworm moth, Bombyx mori








What is a standard brain?

Standard brain is a brain image and map with aveage shape and geometry. We obtained an average outline shape of moth brain from LSM brain images. Tissue image in the brain was registered  into the average outline shape. Anyone use this image for extracting neuropiles and tracts and registration of segmentaed objects.


Softwares

1)Fiji(http://fiji.sc/Fiji

 

Plug-in softwares

 ・ NIfTI images (nifti_io.jar)

   http://rsbweb.nih.gov/ij/plugins/nifti.html

 ・ Max Entolopy Methods (Entropy_Threshold.class)

   http://rsbweb.nih.gov/ij/plugins/entropy.html

 ・ Thin-plate spline formation (NeuroRegister_.jar) 

   https://invbrain.neuroinf.jp/

 ・ Modeling of extracted modules and neurons (IntSeg_3D.jar)

   http://3dviewer.neurofly.de/

2)ITK-SNAP

   http://www.itksnap.org/pmwiki/pmwiki.php

3)Segmentation softwares


 ・ SIGEN: https://invbrain.neuroinf.jp/modules/newdb2/detail.php?id=68


 ・ KNEWRiTE: https://github.com/sc4brain/knewrite


Provieded Data 

 ・ Brain Images

averageP.tif
overlay1.tif
overlay2.tif
sample1F.points
sample1F.tif
sample2F.points
sample2F.tif
sample3P.tif
sample3Psym.points
sample3Psym.tif
SBimageP.tif
SBShapeP.tif
SBShapeSym.points
SBShapeSym.tif
templateF.points
templateF.tif

transformed1.tif
transformed2.tif

 ・ Antennal Lobe

ALsample1.hdr
ALsample1.img
ALsample1.vtk
ALsample1Seg.nii

 ・ ALregist

ALsample1Seg.nii
ALsample1Seg.points
ALsample1Seg.tif
overlaiedAL.tif
SBimageF.points
SBimageF.tif
transformedAL.tif

 ・ Neuron

BMP
2chika-Fused_Neuron-1.tif
C1-Neuron1a.tif

C1-Neuron1b.tif
D03V05C00S20.swc
D03V05C00S20.vtk
Fused_Neuron1.tif

 ・ NeuronRegist

D03V05C00S20.swc
Fused_Neuron1.points
Fused_Neuron1.tif
registNeuron.swc
registNeuronFlip.swc
SBimageP.points
SBimageP.tif

 ・ NeuronSim

D03V05C00S20.swc


Provided files

We are providing stack image of the standard brain of silkworm moth. Image format is the multi-page tiff. Voxel size of the image stack is 2 micron-meters when the image size is 512x512 and the number of slices is 154. Image files are named by the number of pixel and slices, such as 0512x0512x0154.tif. We are also providing binary, contour image and surface model data (Wavefron Obj format) in the standard brain page.


Gray scale image data

XY direction: 2um/pixel, Z direction: 2um  0512x0512x0154 (40MB)
XY direction: 2um/pixel, Z direction: 1um  0512x0512x0308 (80MB)
XY direction: 0.32um/pixel, Z direction: 2um   3215x3215x0154 (1.59GB)

Extracted slice images between 75 and 80
XY direction: 2um/pixel, Z direction: 2um   0512x0512x0154 (40MB)


Binary image data

XY direction: 4um/pixel, Z direction: 2um   0256x0256x0154 (10MB)
XY direction: 2um/pixel,  Z direction: 2um   0512x0512x0154 (40MB)
XY direction: 2um/pixel, Z direction: 1um   0512x0512x0308 (80MB)


Outline image data

XY direction: 2um/pixel, Z direction: 2um   0512x0512x0154 (40MB)
XY direction: 2um/pixel, Z direction: 1um   0512x0512x0308 (80MB)

Extracted maximum outline image data

XY direction: 2um/pixel   0512x0512 (266KB)


3D Surface model (Wavefront .obj format)

Detail model   obj file (34MB),   mtl file (4KB)
Simple model   obj file (13MB),   mtl file (4KB)
Mini model   obj file (5MB),   mtl file (4KB)
Tiny model   obj file (2MB) ,   mtl file (4KB)


Regions

References

Development of a Scheme and Tools to Construct a Standard Moth Brain for Neural Network Simulations, Hidetoshi Ikeno, Tomoki Kazawa, Shigehiro Namiki, Daisuke Miyamoto, Yohei Sato, Stephan Shuichi Haupt, Ikuko Nishikawa, and Ryohei Kanzaki, Computational Intelligence and Neuroscience, 2012 (2012), Article ID 795291, doi:10.1155/2012/795291, http://www.hindawi.com/journals/cin/2012/795291/


updating of the site
Copyright (C) 2018 Neuroinformatics Unit, RIKEN Center for Brain Science