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, Linux support added thanks to @hedjour

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

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!

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. Then simply double click the .sh file of your choice.

Mac-OSX

You need to right-click a .command file and select Open. Then you can force the execution of the scripts. Otherwise the OS will prevent you from executing the scripts. Do not double-click the .sh files since it will open a text editor.

If you get an error message, please grant the terminal application with full disk access

Linux

Simply execute the sh scripts.

Scripts help

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

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

Installation Path

Each script can take a path as an argument for the installation. Otherwise a path will be asked. We highly recommend the following path:

• Windows: C:/
• Mac-OSX: /Applications/
• Linux: /user/.Abba/

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

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

Scripts hierarchy

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.

install_warpy 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

And specify a path.

Fiji

full_install_biop_fiji

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

install_fiji

Downloads Fiji and updates it.

install_fiji_update_sites

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

QuPath

full_install_biop_qupath

Warning: Fiji needs to be installed on the same path

This script downloads and install QuPath version v0.4.4.

install_qupath

Downloads QuPath and installs it.

install_qupath_extensions

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

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

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

install_abba

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 PTBIOP 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 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

This script can be executed after install_abba 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.