Single cell analysis GUI

The tool provides an interactive GUI that wraps up computational methods for single cell analysis into a step by step pipeline. Reference: https://www.biorxiv.org/content/10.1101/510222v1

Installation:

GUI:

git clone https://github.com/Ren22/1c_gui_complete.git

Main package with the computational methods:

git clone https://git.embl.de/nigmetzi/spaceM.git

Put both directories into one next to each other.

Common to all systems:

• Use provided requirements.txt file from ./env_files and install it with pip:

pip install -r requirements.txt

• Install metaspace package from github

• Install Fiji 2014 June 02

Install Cellprofiler 3.1.8

Ubuntu:
Install Cellprofiler 3.1.3 into the conda environment

Requirements:

As datasets can be quite heavy to process make sure you are using minimum:

• RAM: >=16 Gb
• CPUs: >=4