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An iFISH probe design pipeline, with web interface included.

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iFISH-Probe-Design (ifpd) is a Python3.7+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It also includes a web interface, which simplifies the procedure by removing any requirement for programming skills. Read the online documentation for more details.


iFISH-Probe-Designer is fully implemented in Python3.7+, thus you need Python3 to run it. Check out here how to install Python3.7+ on your machine if you don't have it yet.

ifpd has been tested with Python 3.7, 3.8, and 3.9. We recommend installing it using pipx (see below) to avoid dependency conflicts with other packages. The packages it depends on are listed in our dependency graph. We use poetry to handle our dependencies.


We recommend installing ifpd using pipx. Check how to install pipx here if you don't have it yet!

Once you have pipx ready on your system, install the latest stable release of ifpd by running: pipx install ifpd. If you see the stars (✨ 🌟 ✨), then the installation went well!


All iFISH-Probe-Design commands are accessible via the ifpd keyword on the terminal. For each command, you can access its help page by using the -h option. More details on how to run ifpd are available in the online documentation.


We welcome any contributions to ifpd. In short, we use black to standardize code format. Any code change also needs to pass mypy checks. For more details, please refer to our contribution guidelines if this is your first time contributing! Also, check out our code of conduct.


  • Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., ... & Bienko, M. (2019). iFISH is a publicly available resource enabling versatile DNA FISH to study genome architecture. Nature communications, 10(1), 1-15. (link)


MIT License - Copyright (c) 2016-21 Gabriele Girelli

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