RegenSeq Open Source Community
Transform Obsolete DNA Sequencers into Cutting-Edge Automation Platforms
RegenSeq is an NSF-funded open source ecosystem that repurposes decommissioned Illumina HiSeq 2500 DNA sequencers into flexible automation platforms for spatial biology research.
About RegenSeq
RegenSeq gives decommissioned Illumina HiSeq 2500 instruments — once costing hundreds of thousands of dollars — a second life as flexible laboratory automation platforms. By replacing proprietary sequencing chemistry with open protocols, researchers can run multiplexed immunofluorescence, spatial transcriptomics, and proteomics workflows on hardware available for a fraction of its original price on the secondary market.
The project is built around PySeq2500, a fully open Python library that exposes direct control over the instrument's fluidics, temperature regulation, and four-channel fluorescence imaging system. Because every protocol is an editable Python file, researchers can adapt experiments without specialized engineering knowledge, accelerating the development of novel single-cell and spatial biology assays.
Repurpose & Reuse
Convert decommissioned Illumina HiSeq 2500 sequencers — once costing hundreds of thousands — into accessible research tools available on the secondary market.
Advanced Automation
Precise control of temperature, fluidics, and imaging for complex spatial biology applications including multiplexed immunofluorescence and proteomics.
Open Source
Fully open Python codebase with customizable protocols — no specialized engineering expertise required. Community-driven development and support.
Technical Capabilities
PySeq2500 exposes every subsystem of the HiSeq 2500 through a clean Python API, letting researchers compose complex multi-day experiments from simple, reusable building blocks. The capabilities below make the platform suitable for applications ranging from cyclic immunofluorescence to in-situ sequencing.
- 4-Channel Imaging — Simultaneous multi-channel fluorescence image acquisition with precise positioning.
- Temperature Control — Integrated stage temperature control for stable, reproducible experiments.
- Automated Fluidics — Programmable reagent exchange with precise pump and valve control.
- Custom Flow Cells — Inexpensive, easily assembled flow cells compatible with standard samples.
- Python-Based Protocols — Editable configuration and protocol files for complete experimental control.
- Multi-Day Workflows — Stable operation over extended experiments with unattended execution.
NSF POSE Phase 1 Grant — Creating an Open Source Ecosystem
The NSF Pathways to Enable Open-Source Ecosystems (POSE) Phase 1 award supports RegenSeq in transitioning from a single-lab research tool into a fully open, community-maintained ecosystem. The grant funds governance planning, community outreach, and the infrastructure needed to sustain the project beyond its founding institution at the New York Genome Center.
By making high-throughput spatial biology accessible to laboratories that cannot afford commercial platforms, RegenSeq directly addresses equity gaps in the life sciences.
Broader Impacts
- Accessibility — Increase throughput and accessibility of advanced single-cell assays, enabling broader research communities to generate high-quality data for studying diseases like cancer and neurodegeneration.
- Democratization — Lower cost and expertise barriers to automation, expanding access to cutting-edge methods beyond elite institutions and democratizing scientific research.
- Sustainability — Model sustainable resource management by repurposing obsolete scientific instruments, fostering collaboration and environmentally responsible innovation.
- Transparency — Give users full control over data and processing, enhancing transparency, security, and privacy compared to commercial closed-box platforms.
Leadership Team
RegenSeq is led by a multidisciplinary team combining expertise in engineering, biology, software development, and open-source community building, all based at or affiliated with the New York Genome Center.
Dr. Kunal Pandit — Technical Lead
Senior Research Engineer at the New York Genome Center and principal author of RegenSeq's open-source PySeq2500 control software. Dr. Pandit leads hardware integration and instrument control development, enabling researchers to run custom spatial biology protocols on repurposed Illumina HiSeq 2500 sequencers. Contact: kpandit@nygenome.org
Dr. Maros Pleska — Co-Technical Lead
Research Scientist at the New York Genome Center specializing in spatial transcriptomics and proteomics. Dr. Pleska applies RegenSeq workflows to multiplexed imaging experiments and contributes expertise in image processing and single-cell data analysis to the project. Contact: mpleska@nygenome.org
Dr. Daniel Domovic — Entrepreneurial Lead
Scientific Program Manager at the New York Genome Center with a computer science background. Dr. Domovic drives community outreach, partnership development, and stakeholder coordination, helping transition RegenSeq from a single-lab tool into a sustainable open-source ecosystem. Contact: ddomovic@nygenome.org
Kaspar Bumke — Industry Mentor
Electronic engineer and software developer at Kitspace, an open-source platform for sharing electronics designs. Kaspar brings deep expertise in open hardware community building and has made major contributions to the OpenFlexure microscope project, advising RegenSeq on ecosystem governance and open-source best practices. Contact: kaspar@kitspace.org
Get Started
Visit our GitHub repository: https://github.com/nygctech/PySeq2500
Documentation: https://pyseq2500.readthedocs.io
Protocols: https://protocols.io/workspaces/regenseq
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