Conda is a package and environment management system that allows you to:
Install the correct version of Python to run your software
Install software without admin rights (useful for shared machines and compute clusters).
Install software without affecting anyone elses software installation (e.g. on a shared machine).
Install software without potentially messing up any important software on your machine.
Install multiple (potentially conflicting) versions of software at the same time, and allow you to switch between the two. This is very useful if you want to keep using a specific version of software for one experiment, but try out some new features of the latest release for another.
You don't have to use conda, but it will make your life much easier, and it will make it much easier for me to provide help.
You must run conda activate ENV_NAME whenever you open a new terminal window to use your software. If you don't see the (ENV_NAME) part of the prompt, the environment isn't activated
The reason why we use conda environments (other methods other than conda are available) is to have separate Python installations. This way anything we do in the cellfinder environment shouldn't affect any of the other environments.
If anything goes wrong, and cellfinder stops working (and can't be fixed), you can simply make a new environment, and start again. If you have any troubles though, please get in touch.