Please read the following instructions carefully to prepare for the workshop. Completing these steps prior to the workshop is essential to ensure we stay on schedule. If you are having any trouble with the below instructions, please reach out for help:
- For issues with FIJI, contact Sara (sara.salgueirotorres@crick.ac.uk)
- For conda or ilastik issues, contact Stefania (stefania.marcotti@crick.ac.uk)
Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
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Download FIJI from here. Please select the Stable distribution (as opposed to the Latest one).
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To avoid any permissions issues, install FIJI is in your home directory:
- PC:
C:\users\<your user name> - Mac:
/Users/<your user name>
WARNING: FIJI must be installed in a location where it has write permission - otherwise, it cannot update itself
- PC:
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Start FIJI and allow the updater to run:
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(Optional) If the updater does not run automatically, select
Help > Update:
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If FIJI produces any error messages, it is most likely because it does not have the necessary permissions to update itself - return to step #2 and double-check the location of the installation.
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Install Miniconda by following the installation instructions for your operating system at this page. Choosing the "Graphical installer" option should make it easier, if you're not familiar with using the terminal.
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[Windows users only] When prompted, make sure to select "Register Miniconda3 as my default Python 3.13", if not already selected.
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Please check that the installation worked properly by opening the Terminal (MacOS) or Anaconda PowerShell Prompt (Windows) and typing
conda list. If conda has been installed correctly, a list of installed packages appears.
FAQ: "What should I do if I already have conda installed on my machine?"
Please make sure that your conda installation is up to date. To do so, run the following command:
conda --version
If this returns a version older than 23.10.0, please update your conda by running:
conda update -n base conda
- Install ilastik by following the installation instructions for your operating system at this page.
- ilastik should now be available in your Applications or Programs menu. Double-clicking on the its icon should open a page that looks like this:
- Go to https://github.com and follow the “Sign up” link at the top-right of the window.
- Follow the instructions to create an account.
- Verify your email address with GitHub.
- Configure multifactor authentication. More information is available on the relevant GitHub documentation.