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How to get cellfinder installed on your machine. |
If you know what you're doing (and your GPU is set up), just run:
pip install cellfinder{% hint style="info" %} If you're not completely sure what you're doing, read on. {% endhint %}
To run cellfinder you will need a fairly high-powered computer running Windows or Linux (see system requirements for details).
If you don't have access to a high-powered computer, your institute may have a compute cluster you can access. Get in touch with them, and forward them the cluster installation page.
For some aspects (e.g. setting up your GPU), you may also need admin rights to your computer.
Before installing cellfinder I recommend installing some other software first.
cellfinder is written in Python, and so needs a functional Python installation. Your machine may already have Python installed, but I recommend installing miniconda.
See Using conda for details.
{% hint style="danger" %} cellfinder should run on any type of Python installation, but if you don't use conda, I may not be able to help you. {% endhint %}
cellfinder doesn't need to use your GPU (graphics card), but if you have a supported card (most recent NVIDIA cards), it can run much, much faster with it.
See Setting up your GPU for details
{% hint style="info" %} Remember to activate your conda environment before doing anything {% endhint %}
Open your terminal, and activate your conda environment
conda activate cellfinderThen install cellfinder (this could take a few minutes depending on the speed of your network connection).
pip install cellfinderWhen you run cellfinder, it will download the files it needs (atlas, trained machine learning models etc.). If you want to save time later, or you know you won't have an internet connection when you run cellfinder, you can download these in advance. See downloading files for details.