Java Software Engineer for Microscope Control and Image Analysis

Lab Vision

The Discovery Machine Lab led by Loic Royer at the Chan Zuckerberg Biohub will design and build lightsheet microscopy based ‘discovery machines’ that will not only acquire image data, but also perform online processing, instant 3D visualization, adaptive imaging, and automated photo-manipulation. These integrated instruments bring together state of the art optics, robotics, machine learning, and image analysis with the aim of building comprehensive atlases of development and modeling complex cellular choreographies. This new technology will enable Biological discoveries that will lay down the fundations for tomorrow’s medical breakthroughs.

Opportunity

We are looking for a software engineer to join the Discovery Machine Lab and help us build systems to control microscopes, as well as write image analysis and processing algorithms for “closed-loop” smart microscopy. This is an excellent opportunity for a talented, creative, and curious engineer to join a dynamic team advancing science at a world-class research institute.

What we provide

The resources to conceive disruptive technology and obtain ground-breaking results.

Collaborative environment with access to talent and resources of the Biohub platforms

(Bioengineering, Data Sciences, and Advanced Imaging).

Access to collaborators, resources and facilities at Stanford, Berkeley and UCSF.

Excellent, innovative benefits package including open vacation

Fully stocked kitchens and state of the art facilities in a beautiful bayside setting

Responsibilities

Develop software applications to control robotic/automated microscopy systems

Build new or integrate existing image processing, image analysis, control algorithms

Write or adapt real-time deep learning algorithms for microscopy

Connect with a growing international community of open source developers (FiJi, ImgLib2, ClearVolume, ClearControl, Scenery, …) and travel to hackatons.

Interface Java framework with C/C++ device drivers

Improve JavaFX based GUIs

Collaborate with Lab’s microscope builder on instrument control

Collaborate with the Biohub’s Bioengineering team on instrument control

Collaborate with the Biohub’s DataScience on backend storage and processing

Requirements

The ideal candidate for this position loves to acquire new skills and knowledge, thinks creatively, and thrives on engaging in risky but potentially rewarding projects.

Mandatory:
Programming is your first language and you love to build software and/or control robots

Experienced with image processing and analysis.

At least 5 years of Java or C++ programming experience and have the know-how to handle large collections of interdependent projects ( >10 projects >500 classes total)

Experience with Java software engineering projects and familiarity with tools and frameworks such as Gradle and Eclipse.

Desired:
C++/ Labview / OpenCL / OpenGL

Familiarity with the FiJi / ImageJ / ImgLib2 / ClearVolume / KNIME ecosystem

Computer vision and image processing experience

Experience in controlling hardware via device drivers using C/C++ libraries interfaces

GPU-based (OpenCL) image processing and analysis algorithms

Software and hardware interfacing

Computer Graphics: 3D Volume rendering

Notions of Digital and analog electronics for instrument control

Robotics

Physics knowledge, ideally optics and mechanics

Signal processing