** 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 3-Dimensional Model of Early-Stage Zebrafish Embryo Midbrain-Hindbrain Boundary Authors: Ana C. Chang-Gonzalez, Holly C. Gibbs, Arne C. Lekven, Alvin T. Yeh, and Wonmuk Hwang TO BE PUBLISHED (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/
holly-c-gibbs/brain-mesh-builder
Construct surface mesh models based on 3D image stacks of brains
C++GPL-3.0