Getting started

Coppafish

Coppafish is an open source data analysis software for COmbinatorial Padlock-Probe-Amplified Fluorescence In Situ Hybridization (coppafish) datasets. A series of 3D microscope images are arranged into tiles, rounds and channels. For each sequencing round, every considered gene is fluoresced by a dye. By the end of all rounds, each gene has a unique, barcode-like sequence of dyes, called the gene code. For more details about coppafish's methodology, see the overview. See installation on how to install our software, and usage to run coppafish on your dataset. Some vocabulary might be unfamiliar, please see the glossary for reference.

Installation

Prerequisites

Windows or Linux operating system. MacOS is not tested.
At least 48GB of RAM for tile sizes 58x2048x2048.
Python version 3.9 or 3.10.
Git.

Environment

Install coppafish software from within an environment. This can be a venv or conda (recommended) environment.

Conda

For conda, build an environment by doing:

conda create -n coppafish python=3.10
conda activate coppafish

Install

Our latest coppafish release can be cloned locally

git clone --depth 1 https://github.com/reillytilbury/coppafish

install package dependencies and coppafish by

cd coppafish
python -m pip install --upgrade pip
python -m pip install -r requirements.txt
python -m pip install .

Updating

Coppafish will not automatically install updates, but you will see a warning at the start of a pipeline if a new online version is available.

If you already have the source code downloaded, navigate inside of the coppafish directory, then git pull the latest code changes. Then, follow the install steps again, excluding the git clone command, while inside your coppafish environment.

If you do not have the source code downloaded anymore, follow all the install again while inside your coppafish environment.

You can verify your install by running pip show coppafish in the coppafish environment to check you have the latest version.