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n.horner edited this page Apr 23, 2020 · 46 revisions

Requirements

  • A fairly modern PC with a good amount of RAM (16/32GB +).
  • Linux installed on it (We use Ubuntu 18.04) or a Windows PC.
  • Python3.6+
  • It should work on Mac, but it's not been tested.

Linux installation

$ lama/install_LAMA.sh

The above script will install pip3, elastix, R, and LAMA

1) Installation method 1 (recommended) Install LAMA via pip

Install pip, if needed.

sudo apt install python3-pip

Install via pip

pip3 install lama_phenotype_detection --user

### 2) Installation method 2 Clone the git repository ###

```bash
$ git clone https://github.com/mpi2/LAMA.git

Install dependencies listed in Pipfile (you can use pipenv for this)

Give executable permission to the scripts, and add lama_phenotype_detection to your PATH

$ chmod -R u+x scripts/ utilities/

Install programs that LAMA needs

R For statistical analysis. elastix For doing the registrations.

elastix can be installed via apt in Ubuntu 18.04, However it appears to be compiled without support for a metric needed for inversion of images so download the binaries from github.

Check that elastix is installed

source ~/.bashrc
elastix

If installed correclty you will get a message like: Use "elastix --help" for information about elastix-usage.

Check that R is installed

foo@bar:~$ R
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" ...

Check that LAMA is installed correctly

foo@bar:~$ lama_reg
usage: The LAMA registration pipeline [-h] -c CONFIG ...

Windows installation

Install dependencies

Aanaconda 3.6+

https://www.anaconda.com/distribution/

R

https://cran.r-project.org/bin/windows/base/

elastix

Download and unzip elastix from here: https://github.com/SuperElastix/elastix/releases/download/4.9.0/elastix-4.9.0-win64.zip

Add elastix to your path:

  • Control panel > Advanced > Environment Variables
  • Select User variables > Path, then edit
  • Then browse for the folder containing the elastix binaries to add it to the path

Install LAMA

open the Anaconda Prompt

pip install lama_phenotype_detection

Next steps

  • Take a look at the LAMA workflow to see how to run phenotype detection pipeline
  • Run the walkthroughs on some real data to get a feel of how the pipeline works.
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