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 method. 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
venv
python -m venv /path/to/new/virtual/environment
then, in Linux and MacOS:
source /path/to/new/virtual/environment/bin/activate
or windows:
/path/to/new/virtual/environment/Scripts/activate.bat
Install
Our latest coppafish release can be cloned locally
git clone --depth 1 https://github.com/reillytilbury/coppafish
to install the optimised, pytorch GPU and CPU support
cd coppafish
python -m pip install --upgrade pip
python -m pip install -r requirements-gpu.txt
python -m pip install -e .
By default, the GPU will be used if available, otherwise coppafish will revert back to the CPU. For the optimised, pytorch CPU-only support
cd coppafish
python -m pip install --upgrade pip
python -m pip install -r requirements.txt
python -m pip install -e .
If you do not wish to keep a local copy of coppafish (i.e. not interested in git pull
ing higher coppafish versions
later) then remove the -e
option. The source code can then be deleted after installing.
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 right
version.