Sim-FISH

Getting started

To avoid dependency conflicts, we recommend the the use of a dedicated virtual or conda environment. In a terminal run the command:

$ conda create -n simfish_env python=3.6
$ source activate simfish_env

We recommend two options to then install Sim-FISH in your virtual environment.

Download the package from PyPi

Use the package manager pip to install Sim-FISH. In a terminal run the command:

$ pip install sim-fish

Clone package from Github

Clone the project’s Github repository and install it manually with the following commands:

$ git clone git@github.com:fish-quant/sim-fish.git
$ cd sim-fish
$ pip install .

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API reference

Simulations

• Image simulation
• Pattern simulation
• Utility functions

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Support

If you have any question relative to the package, please open an issue on Github.

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Citation

If you exploit this package for your work, please cite:

Imbert A, Ouyang W, Safieddine A, Coleno E, Zimmer C, Bertrand E,
Walter T, Mueller F. FISH-quant v2: a scalable and modular tool for smFISH
image analysis. RNA (2022). doi: 10.1261/rna.079073.121.