fishtools

A Python package for analysing microscopy data for FISH.

Installation

Instructions for installation in Linux or Linux environment in Windows (WSL)

step 1 - Clone repository

Clone or download the code repository.

step 2 - Install bftools

Next install bioformats tools:

bash install-bftools.sh
export PATH=$PATH:~/packages/bftools
bfconvert -version

The last command checks that the install has worked by printing the bioformats version.

If there is a problem running this, you may need additional software. Try installing the additional needed software if missing:

sudo apt update
sudo apt upgrade
sudo apt install unzip
sudo apt install openjdk-11-jdk

(sudo means you have to give the password) Now try the commands to install bioformats tools again.

step 3 - Create Python virtualenv

Test you have working python

python --version

You might need to write "python3" instead of "python". This should print out the python version. Make sure the python version was 3.

Create the Python virtual environment:

python -m venv venv
source venv/bin/activate

If this does not work, you may have to install some software:

sudo apt install python-venv

Install requirements:

pip install -r requirements.txt

This might take a while.

step 4 - Test image conversion

To test the image conversion, first create a folder called local-data. Then copy some test .czi files into that folder. Then, to test the conversion:

mkdir scratch
python scripts/quick_convert_to_ids.py local-data scratch myids

step - OPTIONAL

For Windows WSL In case you need to use a folder not in your home directory you need to mount it so that your computer recognises it. The first time you need to do this (e.g. for a hypothetical drive Z)

mkdir /mnt/z

Each time you restart WSL you may have to do this:

sudo mount -t drvfs Z: /mnt/z

To go into this folder:

cd /mnt/z/