BIOP BASH SCRIPTS

This repository contains bash scripts which should ideally simplify your life when working with QuPath and Fiji.

Windows and Mac-OSX supported, contributions for Linux welcomed!

These scripts should automatically download (internet connection required!), install, update and configure several tools, in a platform independent manner.

If you have issues with these scripts, please post your issue with as much details as possible (script used, your OS + error messages) in forum.image.sc

You can get a help for any of these bash scripts with: ./myscript.sh -h

For Windows, you need to install the 64bits version of Git4Windows in order to execute these bash scripts. (.sh files). You can keep all settings to the default ones with the installer.

To execute scripts, download the full repository as zip (green Code button > Download ZIP) and do not forget to unzip the zip file before running any of these scripts!

You have to close Fiji and QuPath when executing these scripts. Otherwise jars cannot be deleted correctly during updates.

Each script requires a path as an argument for the installation. We recommend the following path:

Windows: C:/
Mac-OSX: /Applications/

If you install on a path with space characters, use double quotes, for instance:

./full_install.sh "C:/Program Files/"

If you execute a script without specifying any path, you will be asked for one.

The full_install* scripts are executing sequentially downstream install scripts. If you are interested in Fiji only, you can directly execute a downstream script (like only install_fiji).

The way scripts are calling one another is shown below:

full_install
├── full_install_biop_fiji
│   ├── install_fiji
│   └── install_fiji_update_sites
├── full_install_biop_qupath
│   ├── install_qupath
│   └── install_qupath_extensions
└── full_install_abba
    ├── install_abba (which install Fiji and QuPath)
    └── install_abba_atlases

If you run the full_install script you will thus run all scripts sequentially, except install_warpy.sh.

install_warpy.sh is an isolated script because it is installing a subset of the components of ABBA. So, if you use install_abba, you will get Warpy as well, but if you want Warpy only, you can use the warpy script instead.

Running scripts multiple times is safe. Pre-installed components are automatically detected and will not be downloaded a second time. However Fiji is always updated multiple times for each re-run, which can take some time.

I want it all!

If you want a machine set up with Fiji and QuPath and extensions like the default one we have at the facility, just run:

./full_install.sh

And specify a path.

Fiji

full_install_biop_fiji.sh

This script downloads, updates and installs Fiji version with a selection of update sites.

install_fiji.sh

Downloads Fiji and updates it.

install_fiji_update_sites.sh

Adds a selection of update sites to the predownloaded Fiji. To know (or modify) the list of updates, check the install_fiji_update_sites.sh script on a text editor.

QuPath

full_install_biop_qupath.sh

Warning: Fiji needs to be installed on the same path

This script downloads and install QuPath version v0.3.1.

install_qupath.sh

Downloads QuPath and installs it.

install_qupath_extensions.sh

Warning: Fiji needs to be installed on the same path This is because the qupath extensions are installed from Fiji. This script adds a selection of extensions to QuPath (check the help to get the list).

Warpy

install_warpy.sh

This script downloads, install, and configure all components needed to use Warpy:

Fiji (+ Bigdataviewer-Playground update site)
QuPath (+ Warpy extension)
Elastix

ABBA

full_install_abba.sh

This script downloads, install, and configure all components needed to use ABBA.

install_abba.sh

This script simplifies the installation of ABBA

With a manual install on windows, one would need to:

install Fiji

install QuPath

install vc_redist_64.exe (necessary for elastix)

install elastix and transformix

enable the ABBA update site on Fiji

set the elastix path on Fiji

install the qupath ABBA extension in QuPath

The full procedure is explained here: https://biop.github.io/ijp-imagetoatlas/installation.html

With this script, you can simply run ./install_abba.sh and all of the procedure above, including the downloads, will be performed automatically.

This script internally uses the scripts InstallQuPathExtension.groovy and SetElastixPath.groovy, which are run within Fiji.

If you prefer a half automated install for more flexibility on the software installs, check https://github.com/enassar/ABBA-QuPath-utility-scripts, which performs automated downloads.

install_abba_atlases.sh

This script can be executed after install_abba.sh in order to pre-download the Allen adult mouse brain atlas CCFv3 and the Waxholm Space atlas of the Sprague Dawley Rat Brain V4. If you do not use this script, the download can be started from Fiji directly.

JTpath/biop-bash-scripts