Senior Image Analysis Software Engineer

Nick Gilbert Neurofibromatosis Research Institute; Detroit (MI); On-site; USD 150,000 - 210,000; Full time

Job summary

The Nick Gilbert Neurofibromatosis Research Institute (NGNRI) in Detroit invites applications for a Senior Image Analysis Software Engineer. You will lead AI/ML powered image analysis for high-content microscopy, turning terabyte-scale data into actionable biological insights.

You will advance state-of-the-art methods for 2D/3D organoid imaging, build scalable pipelines on HPC infrastructure, and ensure rigorous validation and documentation while collaborating with a cross-disciplinary team.

Qualifications

• M.S. or higher in a relevant field; strong Python software skills.
• 2+ years building complex image analysis algorithms.
• Experience with large-scale datasets and scientific workflows.
• Experience training/deploying deep learning models (PyTorch) in real-world settings.
• Familiarity with microscopy data and bioimage tooling.

Responsibilities

• Lead design and implementation of AI/ML image analysis software for 2D/3D organoid imaging.
• Develop robust, scalable pipelines for terabyte-scale datasets on HPC infrastructure.
• Ensure reproducibility, validation, and QC with benchmarks and tests.
• Collaborate with scientists and core teams to align software with research needs.
• Mentor junior engineers and contribute to Open Source bioimage community.

Skills

Python

Deep learning

Image analysis

PyTorch

HPC

Version control

Communication

Education

M.S. in CS/Computational Biology/ Bioinformatics

Ph.D. in CS/Computational Biology (preferred)

Tools

scikit-image

Napari

OMERO

CellProfiler

Fiji/ImageJ

OME-Zarr

Docker

Apptainer

Job description

The Senior Image Analysis Software Engineer role is a rare opportunity to push the AI/ML envelope on mission-critical biological data and see the methods you build go from prototype to daily use by the institute's scientists. The successful candidate will lead the design and implementation of the image analysis software that powers NGNRI’s high-content microscopy screening platform, turning terabyte-scale imaging datasets into therapeutically relevant biological insights.

The role spans the full arc from algorithm to deployment: adapting and advancing state-of-the-art deep learning and image analysis methods for 2D and 3D analysis of cell organoids, and building the robust, high-throughput pipelines that run them on NGNRI’s state-of-the-art High-Performance Computing infrastructure. The role sits within a small, close-knit Digital Team that works in tight collaboration with the Director of Screening and High Content Analysis, the institute’s Data Steward, and the CSO’s wet-lab groups – a deliberately interdisciplinary environment, low on bureaucracy and high on shared ownership. NGNRI actively engages with the Open Source bioimage and scientific computing community, and contributes tooling and algorithms back to it where possible.

This is a senior research software engineering position with a clear mandate: to deliver the production-grade, AI-powered image analysis capabilities at the heart of NGNRI’s Digital Ecosystem, accelerating the discovery of therapeutic targets and compounds for NF1 and related neurological disorders.

About the role

• Lead the design and implementation of the AI/ML-powered image analysis software that powers NGNRI’s high-content microscopy screening platform
• Develop, adapt, and advance state-of-the-art deep learning and classical algorithms for the analysis of 2D and 3D images of cell organoids (e.g., de-noising, segmentation, feature extraction, classification, phenotypic pattern recognition)
• Build robust, scalable analysis pipelines that ensure reliable and fast processing of terabyte-scale image datasets on NGNRI’s High-Performance Computing (HPC) infrastructure
• Ensure reproducibility, validation, and quality control of analysis pipelines through benchmarking, automated testing, and version control
• Partner closely with lab scientists, the Director of Screening and High Content Analysis, and the wider Digital Team to align software development with evolving research needs
• Contribute to the design of image data management, metadata, and storage workflows that ensure accessibility, integrity, and long-term reusability of imaging data (FAIR principles)
• Apply and promote modern software engineering best practices, including code review, continuous integration, and clear technical documentation
• Help recruit and mentor junior engineers, and partner with PhD- and postdoc-level methods developers so they can be productive on NGNRI’s infrastructure
• Continuously evaluate emerging algorithms, frameworks, and tools in computational imaging and machine learning, and translate the most relevant advances into the NGNRI environment
• Contribute to the interpretation of analysis results and to scientific communication, including publications and internal knowledge sharing

About you

Minimum Qualifications

• M.S. degree in Computer Science, Computational Biology, Bioinformatics, Data Science, or a related field4+ years of scientific software development experience in an academic or industry setting, with deep expertise in Python
• 2+ years of experience developing complex image analysis algorithms
• Experience working with large-scale datasets and computational workflows
• Demonstrated experience designing, training, and deploying modern deep learning models in PyTorch in real-world scientific or industrial applications
• Baseline familiarity with microscopy data and core bioimage tooling, or comparable depth in an adjacent imaging domain that transfers cleanly to this setting
• Experience with version control and collaborative software development workflows
• Excellent communication skills, with a demonstrated ability to translate complex algorithmic concepts for non-engineering audiences and to collaborate effectively with PhD- and postdoc-level scientists

Preferred Qualifications

• Ph.D. in Computer Science, Computational Biology, or a related discipline
• Experience with 3D imaging or imaging of organoids
• Familiarity with established image analysis frameworks, libraries, and file formats (e.g., OMERO, scikit-image, CellProfiler, Fiji/ImageJ, OME-Zarr, napari)
• Active engagement with the Open Source bioimage community (e.g., image.sc )
• Experience deploying analysis pipelines on HPC, cloud, or containerized environments (e.g., Docker, Apptainer)
• Exposure to generative AI approaches in scientific imaging

About us

The Nick Gilbert Neurofibromatosis Research Institute (NGNRI) is a nonprofit organization focused on developing treatments and cures for Neurofibromatosis type 1 (NF1) and other neurological disorders and cancers with significant unmet need. Backed by the Gilbert Family Foundation and created in partnership with Michigan State University (MSU) and Henry Ford Health (HFH), NGNRI brings together leading scientific and clinicalexpertiseto accelerate translational discovery.

Located within a new,state-of-the‑artresearch facility in midtown Detroit, NGNRI offers a highly collaborative environment alongside MSU and HFH. The institute is equipped with advanced platforms—including organoid and stem cell models, AI-driven analysis, FACS, and CRISPR technologies—and provides access to extensive shared core facilities.

NGNRI supports both in-house researchers and visiting scientists, creating a dynamic, mission-driven ecosystem designed to advance innovation and deliver impact in an underserved field. As part of Detroit’s rapidly growing medical research campus, NGNRI offers a unique opportunity to contribute tocutting‑edgescience within a vibrant and expanding hub.

NGNRI is in an early stage of development and relies on support from its founding organization, the Rocket Family of Companies, for some of its infrastructure, including talent acquisition. Like the institute itself, salary ranges and benefits are still under construction—they will be highly competitive, commensurate with qualifications and experience.

This job description is an outline of the primary responsibilities of this position and may be modified at the discretion of NGNRI at any time. Decisions related to employment are not based on race, color, religion, national origin, sex, physical or mental disability, sexual orientation, gender identity or expression, age, military or veteran status or any other characteristic protected by state or federal law. NGNRI provides reasonable accommodations to qualified individuals with disabilities in accordance with applicable state and federal laws. Applicants requiring reasonable accommodations in completing the application and/or participating in the application process should contact a member of the Human Resources team, at [e-mail].