F-TGMM

This fork is confirmed to build and run properly with Ubuntu 20.04 LTS and NVIDIA CUDA toolkit 11.1. There are improvements in the image handling and segmentation routines, enhancements to both primary division detection code and to the secondary 3D Haar GPU division classifier, as well as numerous bug fixes in division detection and temporal logical rules.

Quick Start (using pre-built binaries)

System Requirements

• Minimum CPU: 8-core processor (Intel or AMD), 16-core+ recommended
• Minimum RAM: 64 GB, 128 GB+ recommended
• OS: Linux with GUI (has been testing on Ubuntu and Kubuntu from 18.04 to 24.04 LTS)
• Storage: 8 TB+ free space depending on datasets
• GPU: NVIDIA GPU with proprietary driver support, version 470+ (Kepler architecture or newer)
• Minimum CPU: 8-core processor (Intel or AMD), 16-core+ recommended

Instructions

Find the most recent Linux ...build-with-libraries-x86-64.tar.gz archive in Releases on the right column of this page, and save the file to ~/Downloads/F-TGMM.tar.gz. Note: in Linux, tilde ~ is an alias pointing to the user’s home directory (i.e., /home/fred, if username is ‘fred’).

Install to /opt/tgmm using console Konsole/xtern/GNOME Terminal (i.e.Terminal):

sudo mkdir /opt/tgmm
cd ~/Downloads
sudo tar -xvzf F-TGMM.tar.gz -C /opt/tgmm

Install GNU parallel, for running watershed segmentation (ProcessStack) in parallel threads:

sudo apt install parallel

Building F-TGMM

Requirements

• CMake builds with v3.15.3
• CUDA install CUDA toolkit 11.1
• Git to download the software

Instructions

Download the source code:

git clone https://github.com/mhdominguez/F-TGMM.git
cd F-TGMM
git submodule update --init --recursive

Make a build folder and configure the build. Here, we're telling to put the final build products into an "install" folder located next to the build folder.

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=`pwd`/../install ..

Build...

cmake --build . --config Release --target install

And install...

sudo mkdir /opt/tgmm
sudo cp -rf ../install/* /opt/tgmm

Resources

Original TGMM Repository

References

McDole K, Guignard L, Amat F, Berger A, Malandain G, Royer LA, Turaga SC, Branson K, Keller PJ Cell. 2018 Oct 10;175(3):859-876. doi: 10.1016/j.cell.2018.09.031

Amat F, Höckendorf B, Wan Y, Lemon WC, McDole K, Keller PJ Nature Protocols. 2015 Oct 2;10(11):1679-96. doi: 10.1038/nprot.2015.111

Amat F, Lemon W, Mossing DP, McDole K, Wan Y, Branson K, Myers EW, Keller PJ. Nature Methods. 2014 Jul 20;11(9):951-8. doi: 10.1038/nmeth.3036