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Installation.md

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Installation

These installation instructions are very preliminary, and surely will not work on all systems. But if any problems come up, do not hesitate to contact us (ideally via Github issue).

Step 1: Create a virtual environment

Before running any scripts, you should create a virtual Python environment. In these instructions, we use Miniconda for managing your virtual environments, but any alternative like Conda, Mamba, virtualenv, venv, ... should be fine.

If you don't have any, you could install Miniconda from the official website.

Now you can create a new virtual environment using

conda create --name <env_name> python=3.9

In order to use it, you need to activate the environment:

conda activate <env_name>

Step 2: Installation via PyPI (Option 1, recommended)

The easiest way to install MemBrain-pick and its dependencies (except for surforama, see below) is to type

pip install membrain-pick

This should install MemBrain-pick directly from PyPI.

Step 2 alternative: Installation via cloning our repository (Option 2, recommended)

Make sure to have git installed, then run

git clone https://github.com/CellArchLab/membrain-pick.git

Move to the folder "membrain-pick" (from the cloned repository above) that contains the "src" folder. Here, run

cd membrain-pick
pip install .

This will install MemBrain-seg and all dependencies required for segmenting your tomograms.

Step 3: Validate installation

As a first check whether the installation was successful, you can run

membrain_pick

This should display the different options you can choose from MemBrain, like "segment" and "train", similar to the screenshot below:

Step 4: Install surforama

In order to visualize the results of MemBrain-pick, you can use surforama. However, the current official version of surforama has some compatibility issues with the current version of MemBrain-pick. Therefore, it's best to install it via

  1. close repo https://github.com/LorenzLamm/surforama.git
  2. switch to branch "star_file_loading_adjustments"
  3. install via pip install .
git clone https://github.com/LorenzLamm/surforama.git
cd surforama
git checkout star_file_loading_adjustments
pip install .
pip install napari

We are working on a more stable version of surforama that will be compatible with the current version of MemBrain-pick.