autoFISH - automated FISH experiments

Python library to control an automated fluidics system and perform microscope acquisition for iterative FISH experiments.

See dedicated documentation here for how to install and use this package.

TESTED FOR WIN 10 only: micromanager and most microscope controls work only under Windows.

Getting started

Installation

1. Download latest version of miniconda from here (can also be Python 3.X).
2. Open Anaconda terminal and create dedicated environment: conda create --name autofish python=3.9
3. Activate environment: conda activate autofish
4. Pip install pip install -i https://test.pypi.org/simple/ autofish

Starting autofish

1. Open Anaconda terminal and activate environment: conda activate autofish
2. Start user interface with command autofish

Configuration files

The behavior of the fluidics and acquistion system is defined by several config files.

• To test the installation of autofish, you can use demo configurations which require neither a microscope nor a fluidics systems: https://github.com/fish-quant/autofish/tree/main/demo

• We provide config files that we use on our system (with a Nikon Ti): https://github.com/fish-quant/autofish/tree/main/configs

Building the Fluidics system

See dedicated documentation here for how to build the fluidics system.

Reporting a problem/suggestion

If you encounter a problem or you have a suggestion, please file an issue.