Installation¶
For installation instructions in a cluster computing environment, see here
Only tested on Ubuntu 16.04 and 18.04
If required, install CUDA for GPU-support¶
Necessary for training cell classification, highly recommended for inference. For compatibility, we require CUDA 10.1 and cuDNN >=7.6, instructions can be found here. If you need other versions of CUDA (for other work), please see here for how to link CUDA versions to conda environments.
Alternatively, CUDA can be installed into your conda environment (see below).
Set up conda environment and install dependencies¶
Recommended, allthough not necessary Conda environments are used to isolate python versions and packages.
Once conda environment is set up, everything must be carried out in this environment
Download miniconda installation file here
Run miniconda installation file, e.g.:
bash ~/Downloads/Miniconda3-latest-Linux-x86_64.sh
Create and activate new minimal conda environment
conda create --name cellfinder python
conda activate cellfinder
Optional: Install CUDA and cuDNN into the conda environment:¶
This avoids the need to install CUDA and cuDNN system-wide, but the GPU drivers are still required
conda install cudatoolkit=10.1 cudnn
Install cellfinder¶
pip install cellfinder
If you use a conda environment, remember to activate it
(conda activate cellfinder
) before using cellfinder.
Download atlas and trained classification models (optional)¶
When cellfinder runs, the appropriate machine learning models and
reference atlas will be downloaded (if not previously done so). If you would
like to download in advance to save time (or if you will not have an internet
connection) please use cellfinder_download
.
Currently, the only supported atlas is the Allen reference mouse
brain, originally from here.
The atlas will download into ./cellfinder/atlas
.
In the future, other atlases will be available, and you will be able to choose which is downloaded.
If you want to modify the cellfinder download, use:
--atlas-install-path
Supply a path to download the atlas elsewhere. This should also update the defaultregistration.conf
file so that the correct atlas is sourced. Alternatively, use this command to tell cellfinder where an existing atlas is, to save it being downloaded twice. (Requires 20GB disk space)--atlas download path
The path to download the atlas into. (Requires 1.2GB disk space). Defaults to/tmp
.
For developers¶
If you want to edit cellfinder, run tests and build the documentation etc, then use:
git clone --branch dev https://github.com/SainsburyWellcomeCentre/cellfinder
cd cellfinder
pip install -e .[dev]