Electron Tomography ToolKit (ETTK)

Main components:

• virus_segment_membrane: segmentation of closed surfaces using min-cut/max-flow routines
• virus_segment_membrane_select_threshold: visualization of implicit surfaces to assess segmentation quality
• Correlation3DNew: geometric template search constrained to a surface
• CutVolumes3DFromPositions: extraction of sub-volumes from tomograms
• LoopCreateVolumeList: creation of metadata for sub-volume averaging
• Test_Metric_Filter: filtering and masking of sub-volumes
• MPI_Classification: sub-volume alignment, averaging and classification using spherical harmonics

Compilation instructions

1. Go to the desired working directory and save that location into the MYPATH variable

export MYPATH=`pwd`

2. Clone the ETTK repository

git clone git@github.com:nextpyp/ettk.git
cd ettk

3. Build ettk-devel.sif container if needed (sudo access required)

sudo singularity build ettk-devel.sif singularity/ettk-devel.def

4. Enter the development environment (bind paths with -B if needed, e.g., -B /work)

singularity shell ettk-devel.sif

5. Build VTK

mkdir ${MYPATH}/ettk/external/VTK5.10.1/build
cd ${MYPATH}/ettk/external/VTK5.10.1/build
ccmake -Wno-dev -D CMAKE_CXX_COMPILER=/usr/bin/g++ -D CMAKE_C_COMPILER=/usr/bin/gcc ..
	Type "c" for configure
	Type "c" for configure
	Type "g" to generate
make -j 4

6. Build ITK

mkdir ${MYPATH}/ettk/external/InsightToolkit-4.2.1/build
cd ${MYPATH}/ettk/external/InsightToolkit-4.2.1/build
ccmake -Wno-dev -D CMAKE_CXX_COMPILER=/usr/bin/g++ -D CMAKE_C_COMPILER=/usr/bin/gcc ..
	Type "c" for configure
	Type "c" for configure
	Type "g" to generate
make -j 4

7. Build binaries

cd ${MYPATH}/ettk
rm CMakeCache.txt*
ccmake -D ITK_DIR=${MYPATH}/ettk/external/InsightToolkit-4.2.1/build -D VTK_DIR=${MYPATH}/ettk/external/VTK5.10.1/build -D BLITZ_DIR=${MYPATH}/ettk/external/blitz-0.9 -D CMAKE_CXX_COMPILER=/usr/bin/g++ -D CMAKE_C_COMPILER=/usr/bin/gcc .
	Type "c" for configure
	Type "c" for configure
	Type "g" to generate
make -j 4