Installing amap

If you already have cellfinder, then amap has been installed for you.


amap is included with cellfinder. Unless you have a particular reason not to, I would install cellfinder as this will install all the packages you may need. See cellfinder installation.

If you know what you're doing just run:

pip install amap

If you're not completely sure what you're doing, read on.


To run amap you will need a fairly high-powered computer running Windows or Linux (see system requirements for details). In particular, to use some of the atlases, you may need at least 32GB of RAM.

Setting up your machine

Installing Python

amap 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.

amap should run on any type of Python installation, but if you don't use conda, I may not be able to help you.

Installing amap

Remember to activate your conda environment before doing anything

pip install amap

Download atlas (optional)

When you run amap, it will download the files it needs (e.g. the atlas). If you want to save time later, or you know you won't have an internet connection when you run amap you can download these in advance. See downloading files for details.