autoFISH - automated FISH experiments

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

Documentation of this package:

• PDF
• WORD

Documentation to build the fluidics system:

• PDF
• WORD

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

Getting started

Installation

We recommend using a package manager (conda) to maintain a clean Python installation. This nees to be done only once.

1. Download latest version of miniconda from here.
2. Open Anaconda terminal and create dedicated environment: conda create --name autofish python=3.9
3. Activate environment: conda activate autofish
4. Pip install autofish (as an alternative see development installation below)
   • Base version (without pycromanager) : pip install -i https://test.pypi.org/simple/autofish
   • Install pycromanager : pip install pycromanager

Installation for development

If you want to further develop the package, several options exist. A simply one is local installation.

Rather than performing the pip install from pypi (step 4 above), you can install it locally

1. Download the zip archive of the branch you are interested in.
2. Unzip on your machine.
3. Open Anaconda terminal at location of the autofish package.
4. Activate environment: conda activate autofish
5. Editable install pip install . -e

Pycromanager

One of the acquisition options is via Pycromanager. We found that keeping both micromanager and Pycromanager up-to-date can help to prevent problems.

Last tested, compatible versions:

• Pycromanager: 0.27.2
• Micromanager: nightly 20230224

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

Reporting a problem/suggestion

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