The Saalfeld Lab attheHoward Hughes Medical Institute’s Janelia Research Campus is looking for an outstanding software developer to help us create interactive tools and methods for scalable semi-automatic collaborative reconstruction of dense neural tissue from high resolution electron microscopy. We are working with unique cutting edge image datasets from all flavors of electron and light microscopy, tightly interacting with a number of computational and biology labs within the institute and worldwide. We are collaborating with leading experts in machine learning and computer vision on developing new methods for scalable automatic image analysis. We are actively participating in Open Source software development for biological image analysis (ImgLib2, BigDataViewer, CATMAID, TrakEM2, Fiji).
HHMI’s Janelia Research Campus is a pioneering research center near Washington, D. C., where scientists from many disciplines develop and use emerging and innovative technologies to pursue science’s most challenging problems. In particular, Janelia is focused on technologies for biological imaging and understanding neural circuits and how they give rise to behavior. Established in 2006, Janelia was modeled after institutes like Bell Labs, with small groups collaborating on high-risk, high-reward, innovative science.
Example projects being pursued in the lab
- high precision volume assembly and artifact correction from large (>100 Terabytes) serial section/ scanning datasets recorded with Electron Microscopes developed by groups here at Janelia;
- semi-automatic interactive neuron and synapse reconstruction using the BigDataViewer and active learning;
- register multi-modal recordings from the same and across specimens.
Principal Responsibilities
You will co-develop software with lab-members. This includes but is not exclusive to:
- user interface based on ongoing work with the BigDataViewer for collaborative semi-automatic 3D anatomy reconstruction in an active learning framework;
- scalable solutions for synchronizing user interaction, active learning, and automatic reconstruction in very large image volumes;
- scalable solutions for artifact correction in very large image volumes;
- your own interesting project.
Additional Information
For more information about the Saalfeld lab, please visit:https://www.janelia.org/lab/saalfeld-lab. For information about Janelia, please visit:https://www.janelia.org.
Required Qualifications
- BS/MSc in Computer Science, Engineering, Applied Math, Physics or related discipline, and/ or sufficient and demonstrable experience in the field, supported by both source code available online and letters of reference from your supervisors or co-entrepreneurs;
- established collaborative programming skills in at least one high performance programming language (C/C++, Java, ) and debugging fluency in Python, Javascript, Julia or any other scripting language for rapid prototyping;
- candidates will be expected to produce examples of software that she/he has written for evaluation during the interview process;
- knowledge of modern version control and other software engineering practices;
- ability to work and support interdisciplinary work in small lab groups;
- ability to think and learn independently;
- experience with Spark or other modern approaches for high performance computing highly appreciated;
- general interest in neuroscience, biological image analysis, and great user interfaces.
HHNMI is an Equal Opportunity Employer.
