Installation

Using Conda (all platforms)

We recommend using Conda to install STIM. If you don't have Conda installed, please follow the instructions here. Once Conda is installed, you can install STIM from conda-forge by running:

conda install -c conda-forge stim

Building from source (Ubuntu)

Building STIM from source requires maven and OpenJDK8 (or newer). On Ubuntu, you can install them via the default package manager:

sudo apt-get install openjdk-8-jdk maven

Next, please check out this repository and go into the folder

git clone https://github.com/PreibischLab/stim.git
cd stim

The recommended way is to just call the install script without any arguments to install STIM into the checked out directory:

./install

To install into your favorite local binary $PATH (e.g., $HOME/bin) you can call:

./install $HOME/bin

All dependencies will be downloaded and managed by maven automatically. For platforms other than Ubuntu, please find your way and report back if interested.

This currently installs several tools: st-resave, st-add-slice, st-normalize, st-explorer, st-render, st-bdv-view, st-add-annotations, st-align-pairs, st-align-pairs-view, st-align-global.

The process should finish with a message similar to this (here we only called ./install thus installing in the code directory):

Installing 'st-explorer' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-render' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-bdv-view' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-resave' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-slice' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-normalize' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-add-annotations' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-pairs-view' command into /Users/spreibi/Downloads/stim_test/stim
Installing 'st-align-global' command into /Users/spreibi/Downloads/stim_test/stim

Installation directory equals current directory, we are done.
Installation finished.

The installation should take around 1 minute.