Scientist I, Microscopy Image Analysis and 3D Visualization

The mission of Allen Institute for Cell Science is to develop a comprehensive and holistic approach to measure, describe, and model cell states and their dynamic changes over time. Our ultimate goal is to uncover the fundamental principles of multiscale, multicellular morphogenesis, including how groups of cells organize and achieve collective behaviors essential for life. Our approach encompasses multi-modal data collection including live 3D timelapse imaging, data analysis, theory, and predictions to understand cell states and cell state transitions in human induced pluripotent stem cell models. As a division within the Allen Institute, the Allen Institute for Cell Science uses a team-oriented approach, focusing on accelerating foundational research, developing standards and models, and cultivating new ideas to make a transformational impact on science.

We are seeking a highly motivated and goal-oriented Scientist I - Microscopy Image Analysis and Visualization to develop and apply cutting-edge image analysis workflows and visualization pipelines. This role offers a unique opportunity to apply and integrate advanced image processing, computer vision, and data visualization techniques to advance the field of cell science. Working with a team that includes computational biologists, quantitative and modeling scientists, and software engineers, this scientist will help build robust and reproducible frameworks to extract meaningful quantitative information from complex microscopy datasets and present it effectively. This role will collaborate closely with the Institute’s technical and programmatic teams to achieve the Institute’s shared, programmatic objectives.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Essential Functions

• Develop and implement advanced image analysis algorithms, including those leveraging machine learning, for extracting quantitative information from diverse microscopy data, particularly from live 3D timelapse imaging
• Develop and apply scalable visualization pipelines to reveal the complexity of 3D timelapse image data and guide downstream analysis
• Develop robust protocols and reproducible frameworks to generate quantitative information from microscopy image data, with an emphasis on high-throughput and automated analysis
• Apply computational microscopy and computer vision approaches to segment, track, and characterize cellular structures and dynamics in biological systems
• Develop and maintain custom scripts and software tools for microscopy image analysis, data processing, and advanced
• Collaborate with scientists and programs across the Institute to coordinate complex experiments by scaling image analysis and visualization protocols into high-throughput computational pipelines and ensuring the seamless integration and sharing of data and resources
• Maintain rigorous quality control standards and thorough documentation
• Prepare written summaries and present activities internally and publicly
• Adherence to SOPs, GLPs, and regulatory requirements

Required Education and Experience

• PhD in a computer science, biological science (e.g. cell biology, biophysics, bioengineering), physical science, or related science or engineering field; or equivalent combination of degree and experience required
• Extensive knowledge and hands-on experience with machine learning, image analysis algorithms, data visualization techniques, and the development and implementation of deep learning algorithms
• Experience working in a multi-disciplinary environment in academic or industrial settings

Preferred Education and Experience

• Deep knowledge of microscopy imaging modalities, computational microscopy techniques, and image artifacts
• Extensive experience with 3D live-cell and timelapse imaging techniques and data analysis
• Experience with computer graphics, 3D visualization software (e.g., Blender, Paraview, Napari), and developing procedural animations for scientific data representation
• Experience with descriptive modeling and statistical analysis to interpret quantitative image data and generate biological insights
• Experience with deep learning-based segmentation algorithms, object detection, and generative modeling for biological images
• Ability to communicate complex concepts related to AI-driven image analysis, generative models to non-experts, and connect them to biological problems
• Advanced proficiency in Python programming for image analysis
• Experience with developing or contributing to open-source tools/packages for biological image analysis or visualization (e.g., demonstrated via GitHub contributions)
• Familiarity with software engineering practices such as version management, build management, and testing
• Excellent interpersonal skills
• Experience working in a multi-disciplinary environment in academic or industrial settings
• Ability to work both independently and in a collaborative, multi-disciplinary environment
• Careful attention to detail

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment

Position Type/Expected Hours of Work

• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with the flexibility to work remotely on a limited basis

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

• $90,000 - $112,400*

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.