Control suite for the qi2lab 3D MERFISH widefield acquisition platform. This control suite generates data that can be directly processed using our GPU 3D MERFISH analysis processing platform, merfish3d-analysis.
merfish3d-wfacq implements a custom GUI widget, acquisition engine, and file writing code to perform iterative imaging spatial transcriptomics experiments. It is built on top of Micro-Manager and pymmcore-plus.
Documentation, including example input files, is available at https://qi2lab.github.io/merfish3d-wfacq/
Fluidics-only runs execute every round listed in the fluidics program, even when the program contains no RUN rows.
GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments.
Create a python 3.12 environment using your favorite package manager, e.g.
conda create -n merfish3d-wfacq python=3.12
Activate the environment.
conda activate merfish3d-wfacq
Next, clone the repository in your location of choice and enter the directory using
git clone https://github.com/QI2lab/merfish3d-wfacq
cd merfish3d-wfacq
and install using
pip install .
For interactive editing use
pip install -e .
This repository is configured for Zensical documentation.
python -m pip install -e .[dev]
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