Senior/Lead Software Engineer, Medical Instrumentation

Company Description Applikate is an emerging medical device company located in New Haven, Connecticut revolutionizing the practice of pathology. A spin-out from Yale University, our highly innovative, comprehensive, and unique blend of hardware, software and optics enables a technology that is incomparably efficient at automating tissue processing and digital imaging without the need for physical slides.

Join a small, high performance team that is leading a technological revolution in pathology services to improve the quality of patient care through tools that reduce diagnostic error rates, accelerate testing and lower costs.

Role Description Applikate is looking for a Senior/Lead Software Engineer to take a leading role in developing a ground-breaking, patented high-performance laser microscopy system for digital pathology, integrating automated image acquisition, processing and whole-tissue imaging.

This is a hands-on software development position focused primarily on the instrument control backend and graphical user interface, with additional work in image processing and cloud-based image viewing. You will have significant ownership of software architecture and technical decisions as we bring the system to market as a commercial medical device.

As part of a small, highly effective team, you will work across the software stack, implement critical systems, establish sound engineering practices, and contribute to development within a regulated medical device environment.

Responsibilities

• Own and evolve the software architecture, including component boundaries, interfaces, state management, and execution workflows.
• Design and develop backend software supporting image acquisition, instrument workflows, data processing, and order management.
• Build intuitive GUIs for configuring scans, guiding operators through workflows, monitoring system status, and reviewing results.
• Optimize and maintain image-processing pipelines for large microscopy and whole-slide imaging datasets.
• Translate system requirements into software requirements and designs, ensuring traceability to risk controls and verification activities.
• Guide and mentor other engineers through task planning, technical reviews, and collaboration.
• Establish and improve development practices, including automated testing, secure software development, CI/CD, and controlled software releases.

Qualifications

At least 7 years of professional software development experience, including substantial experience developing production software on Linux.

• Demonstrated architectural ownership of complex software applications.
• Experience developing backend systems and interactive applications using desktop GUI or modern web frameworks.
• Strong communication skills and a commitment to building reliable, maintainable, and secure systems.

Direct experience

developing software within a regulated medical-device environment, including:

• IEC 62304 software lifecycle processes, preferably for Software Safety Class B systems.
• Software risk management under ISO 14971 and development within an ISO 13485 quality management system.
• Planning, executing, and documenting software verification and validation activities.

Experience

with most of the following is preferred:

• Python application development, including asynchronous programming
• Microscopy, digital pathology, medical imaging, or machine vision
• C++ or Rust
• Zarr, TIFF/OME-TIFF, DICOM, or whole-slide image formats
• Web application development and cloud deployment, preferably using AWS.
• CI/CD within a controlled or regulated development environment
• Automated integration testing, hardware simulation, or fault injection.
• AI-assisted or agentic software development, with strong testing and review practices.

Benefits & Perks:

• Competitive Salary commensurate with experience
• 401(k) plan
• Comprehensive health insurance
• Equity program
• 11 paid holidays and generous PTO policy
• Local, Hybrid or Remote considered for the right candidate

The office is located in New Haven with easy access to Boston and New York City.

Employment is determined based on merit and skills match. Applikate is an equal opportunity employer encouraging diversity and valuing inclusion.