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Bioinformatics Engineer

S San Francisco, CA 94080

Posted: 11/20/2024 Employment Type: Contract Job Category: Data Sciences Job Number: 616106 Is job remote?: Yes Country: United States

Job Description


Senior Bioinformatics and Image Analysis Engineer
Biology Research | AI Development (BRAID) group

Background & Project
The Biology Research and AI Development (BRAID) group is seeking a highly skilled and innovative bioinformatician and software engineer to drive the development of a modular, Python-based platform for single-cell image processing and analysis. This cutting-edge framework is designed to process raw images from Optical Pooled Screens (OPS), PertubView, and Cell Painting experiments, ultimately generating comprehensive feature tables that enable deep biological insights. Key image processing steps include advanced stitching, precise image registration, denoising, spot detection, read calling, nuclei and cell segmentation, and phenotypic feature extraction. The scope of this platform extends beyond image processing; it encompasses data preprocessing, transformation, statistical analysis, and visualization, creating a robust end-to-end solution for researchers. In addition to developing and optimizing this innovative platform, the role involves the analysis of existing internal projects to enhance methodologies, derive actionable insights, and inform future experiments. This hands-on, collaborative position provides a unique opportunity to work closely with scientists and engineers across disciplines, blending expertise to tackle complex challenges in bioinformatics and image analysis. The role also offers the chance to provide dedicated office hours, supporting internal package users through personalized troubleshooting, user engagement, and hands-on guidance. By facilitating interactions and empowering users, this position contributes to building a thriving, collaborative research community. 

Responsibilities
  • Collaborate with image processing and spatial omics experts to create and optimize a comprehensive image processing and analysis framework, integrating diverse computational needs and methodologies.
  • Develop and maintain a scalable software architecture to support key processes, including image stitching, image registration, denoising, spot detection, read calling, cell segmentation, phenotypic feature extraction, as well as data preprocessing, transformation, statistical analysis, and visualization.
  • Provide regular office hours to support and engage package users, offering personalized troubleshooting, guidance, and training to foster effective software utilization.
  • Work collaboratively with multidisciplinary teams, including local and remote engineering teams, to achieve project milestones and support broader scientific initiatives.
  • Contribute to the broader scientific and open-source communities through impactful software development. Requirements
  • Ph.D. in bioinformatics or computer science.
  • 5+ years of experience developing and optimizing Python-based solutions, with a minimum of 2 years dedicated to building image analysis pipelines for applications such as OPS, PerturbView, and Cell Painting.
  • Expertise in version control systems (e.g., Git) and experience with CI/CD pipelines, actions, and automated workflows.
  • Proven ability to create, deploy, and support complex bioinformatics workflows, including image stitching, image registration, segmentation, data preprocessing, transformation, statistical analysis, and visualization.
  • Strong communication skills for conveying complex scientific and technical concepts to diverse teams and stakeholders.
  • Self-motivated and enthusiastic about programming and tool development.
  • Willingness to work in a Research-motivated environment and learn more about Science.
Preferred Qualifications
  • Experience providing user-facing software support, including guidance, documentation, and direct engagement with scientific users.
  • Familiarity with OPS, including development and application of novel image processing and data analysis tools.
  • Familiarity with the deep learning ecosystem including Pytorch experience.
  • Strong experience with domain-specific image processing and visualization tools like Ahslar, Cellpose, Cellprofiler, Stardist, and Napari.
  • Experience with high-performance computing (HPC), cloud-based workflows, and tools like WDL for workflow orchestration.
  • Knowledge of high-dimensional imaging data models and OPS data structures.
  • Familiarity with Open Microscopy Environment (OME) tools, such as Bioformats, OME-Files, and OMERO.
  • Proven track record of publications in OPS-related fields and significant contributions to open-source projects.
  • Strong initiative, independence, and a passion for exploring and implementing new methodologies and tools 



Pay Rate Range: $45-60/hr depending on experience 

The staffing industry has seen an increase in people falsely representing themselves as recruiters to gather personal information from job seekers. For your safety, do not provide sensitive data to anyone you have not spoken with thoroughly and never provide banking information during the application process. Candidate safety is a top priority at Planet Pharma.

Planet Pharma is an equal opportunity employer. It is our practice not to discriminate against any employee or applicant based on any criteria, condition or basis protected by laws or regulations in the locations where we do business. All qualified applicants are encouraged to apply. We celebrate diversity and are committed to providing an environment of mutual respect. We believe that diversity, equity and inclusion enable us to better meet our mission and values while serving our clients across the globe. If you have a disability or handicap and would like us to accommodate you in any reasonable way, please inform your recruiter, or contact us, so that we can discuss the appropriate alternatives available.

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Although this hasn't been an issue at Planet Pharma, the staffing industry has seen an increase in people falsely representing themselves as recruiters to gather personal information from job seekers. For your safety, do not provide sensitive data to anyone you have not spoken with thoroughly and never provide banking information during the application process. Candidate safety is a top priority at Planet Pharma.