/flybrainaligner

aligning microscope images of fly brains

Primary LanguageC++

flybrainaligner

This repo collects the related software and pipelines developed for aligning fly brains.

Install

Create a folder "Toolkits".

mkdir Toolkits
cd Toolkits
mkdir ANTS
mkdir FSL
mkdir Vaa3D

Install Vaa3D on Linux with Qt4.

With cmake (recommended):

cd vaa3d
./build.cmake -h5j install

With shell script:

cd vaa3d
./build.linux -B -m -j8

Copy "vaa3d" and the "plugins" folder to "Toolkits/Vaa3D"

Install ANTs

mkdir build
cd build
ccmake ..
make -j8

Copy "ANTS" and "WarpImageMultiTransform" to "Toolkits/ANTS".

Install FSL

Download the fsl from the official website and copy "fsl/bin/flirt" to "Toolkits/FSL".

Usage

See brainaligner.

Reference

  1. Peng, H., Ruan, Z., Long, F., Simpson, J.H., and Myers, E.W. (2010) "V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets," Nature Biotechnology, Vol. 28, No. 4, pp.348-353.
  2. Murphy, S. D., Rokicki, K., Bruns, C., Yu, Y., Foster, L., Trautman, E., ... & Clack, N. (2014). The janelia workstation for neuroscience. Keystone Big Data in Biology. san francisco. CA.

Author information

Please contact Yang Yu (gnayuy@gmail.com) if you have any questions.