** DODRI source code files for surface mesh building based on 3-dimensional image stacks

• Authors: Ana C. Chang-Gonzalez and Wonmuk Hwang

• Contact: Wonmuk Hwang, hwm@tamu.edu (see COPYRIGHT.TXT)

• How to cite:

Title: Building a three-dimensional model of early-stage zebrafish embryo brain

Authors: Ana C. Chang-Gonzalez, Holly C. Gibbs, Arne C. Lekven, Alvin T. Yeh, and Wonmuk Hwang

Journal: Biophysical Reports, Volume 1, Issue 1. 100003

Year: 2021

[Source code contents]

./inc/ : program header files ./src/ : *.cpp source files, includes ./io/ folder with IO-related files ./obj/ : compiled object files
./bin/ : dodri executable ./test/ : test files and input datasets

[How to compile]

• Prerequisites:

  • C++ compiler: Although we compiled the code using the GNU g++, since the code uses only C++ STL, any C++ compiler should work.

  • GraphicsMagick++: http://www.graphicsmagick.org/Magick++/ For reading/writing image files.

  • This code has been compiled and tested on the Ubuntu 20.04LTS operating system.

• To compile: make clean make

[To execute/test the code]

NOTE:

0) A basic knowledge of the Linux operating system is desired since commands in the README.txt file in each folder are meant to be entered into a Linux terminal window (BASH environment). In Mac OS, a similar terminal can be used. In Microsoft Windows, a Linux emulation program can be used.

1) Visualization was done mostly using the VMD software.

Go to one of the sub-folders in ./test, and follow instructions in README.txt. Each sub-folder is briefly explained below, in relation to our reference paper.

./test/wt_fixed: Fixed WT embryo used for the "Methods" section (Figs. 1-6 of the paper). (SUGGESTION: start with this folder)

./zf_time_lapse : Live time-lapse embryos (Figs. 7, 8, 10)

./fetal_brain : Human Fetal Brain (Fig. 9; 33 weeks)

• For visualization of the output files, following programs can be used. They can be installed free of charge (see README.txt in the above sub-folders):

  VMD (https://www.ks.uiuc.edu/Research/vmd/)
  Chimera (https://www.cgl.ucsf.edu/chimera/) 
  MeshLab (https://www.meshlab.net/)

[Image data]

• ./test/wt_fixed/ and ./test/zf_time_lapse/ (folders named `in'): Provided by Holly Gibbs, Arne Lekven and Alvin Yeh.

• For ./test/fetal_brain: From brain-development.org/brain-atlases/fetal-brain-atlases/